ISME Workshop - All Congo Genomes
Benjamin Allen, Mikayla A Borton, Zach Crockett
Generated May 14, 2025

Welcome to Narrative for Analyzing Congo Surface Water Bins (ISME Workshop Day 2)

In this tutorial you will start with bins and process them so that you can understand the metabolisms that each is potentially capable of. These bins were generated from metagenomic reads derived from DNA extracted from 8 surface water samples. The reads were then trimmed and assembled with metaspades. The contigs from the assemblies were then used for binning with CONCOCT and MaxBin using abundance counts derived from mapping and optimized with DAStool. The bins from all 8 samples (links below) were then collated into this narrative.

Group Narrative
Group A https://narrative.kbase.us/narrative/186838
Group B https://narrative.kbase.us/narrative/186839
Group C https://narrative.kbase.us/narrative/186842
Group D https://narrative.kbase.us/narrative/186840
Group E https://narrative.kbase.us/narrative/186841
Group F https://narrative.kbase.us/narrative/186844
Group G https://narrative.kbase.us/narrative/186843
Group H https://narrative.kbase.us/narrative/186845

Copy this narrative for your group and fill in the answers the questions associated with each app as a team.

STEP 1) Run CheckM on your bin set to assess genome completion

Questions:

  1. How many medium and high quality bins are in the Congo dataset (see https://www.nature.com/articles/nbt.3893 for information on medium and high quality completion and contamination standards)?

STEP 2) Run dRep on your bin set to dereplicate your genomes

Questions:

  1. What are the default parameters for completion, contamination, and percent identity for dRep in KBase? What version are we using?

  2. How does dRep choose the “best” bin or dRep winner for a cluster?

  3. How many dereplicated MAGs do you have in your dataset?

Dereplicate genomes with dRep - v3.1.0
Dereplicate genomes based on ANI and quality
This app completed without errors in 44m 26s.
Objects
Created Object Name Type Description
CONGO_metagenomes_dRep.240729_assemblies AssemblySet Dereplication results
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/187935
  • results.zip

STEP 3) Run checkM on your dereplicated bin set to assess genome completion

Questions:

  1. What is the highest quality genome? Why is it the highest quality? What is that genomes completeness and contamination?

  2. What is the worst quality genome? Why is it the worst quality? What is that genomes completeness and contamination?

  3. This dataset has bins denoted as Kingdom_Bacteria in the Marker Lineage column. What do you think this means in CheckM?

  4. How should we consider genome quality when looking at the functional annotations of a genome?

Assess Genome Quality with CheckM - v1.0.18
Runs the CheckM lineage workflow to assess the genome quality of isolates, single cells, or genome bins from metagenome assemblies through comparison to an existing database of genomes.
This app completed without errors in 1h 6m 48s.
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/187935
  • CheckM_summary_table.tsv.zip - TSV Summary Table from CheckM
  • full_output.zip - Full output of CheckM
  • plots.zip - Output plots from CheckM

STEP 4) Run GTDB-Tk on your bin set to assess genome taxonomy

GTDB-Tk is a toolkit for assigning taxonomy to microbial genomes. See https://academic.oup.com/bioinformatics/article/36/6/1925/5626182?login=true for details on how GTDB-Tk works, databases used, and output details.

Questions

  1. How many phyla for Bacteria and Archaea are represented in the genome set? List them.

  2. You see a bin with the taxa string dBacteria;pActinobacteriota;cAcidimicrobiia;oIMCC26256;fIMCC26256;g;s__. How do you interpret this taxa string? What does it mean that there is no assigned family, genus or species? What does UBA stand for?

  3. What is the highest unnamed taxonomy level in your dataset? How many MAGs have this classification?

  4. What is the full taxonomy string for your best bin?

STEP 5) Run DRAM on your bin set to assess genome metabolic potential

DRAM is a genome annotation tool, as well as a summarization tool for genome metabolism. See https://academic.oup.com/nar/article/48/16/8883/5884738 for details on how DRAM works, databases used, and output details.

Questions:

  1. A key feature of DRAM is the module summary. Look at the TCA cycle (aka Krebbs) for all your bins. Estimate how many MAGs have 5 or less steps in the TCA cycle (hint roll over the yellow ones and look at the steps).

  2. Note, for electron transport chain (ETC) enzymes, completion is not about steps, but about how complete an enzyme complex is (i.e. does it have all subunits). What criteria do you think makes an enzyme complete?

  3. For today, let’s assume enzyme complexes need at least 50% of subunits to be functional. Complex IV is used for aerobic respiration. These multi-subunit enzymes can either be high affinity (meaning they operate best in microaerophilic, or under low oxygen, conditions) or low affinity (meaning higher oxygen conditions). How many bins do you think have the potential to respire at low oxygen levels? Note the two enzymes (cbb3 and bd ubiquinol) are two separate complexes that confer similar oxygen respiration abilities (for today’s exercise).

  4. Which genomes seem to use aerobic respiration for energy production? Hint: look at ETC - NADH dehydrogenase and complex IV.

  5. Beyond oxygen, examine Nitrogen, Sulfur, Photosynthesis, and other reductases. Which biogeochemical process (as denoted by enzymes for steps in the process- nitrate to nitrite, not complete denitrification) is most represented in your genomes. What is the evidence for this? NOTE: use caution in interpreting thiosulfate reduction- this has been fixed in newer versions of DRAM. Do not use thiosulfate=sulfite step, as this gene can also catalyze other steps (non specific), use EC 1.8.5.5 (thiosulfate to sulfite).

  6. Do you have the key functional gene for methanogenesis?

  7. Why do you have genes for using acetate then? [acetate+>methane, pt 1]. Hint: look up the EC number here. Do you think it is specific to methanogens?

  8. Hydrogen metabolism (either using or producing hydrogen) can be an important ecosystem process. To see this metabolism you need to go to the Distillate. Download metabolism_summary.xlsx file. Go to Energy Tab. Search column D for hydrogenase. Do you have any evidence for this in your data?

  9. What is a CAZyme? What database does DRAM use for annotating CAZymes?

  10. What CAZyme substrates are well represented in your genomes?

  11. Final synthesis and GROUP DISCUSSION. Choose a single bin or MAG. For your bin you will now analyze a genome’s metabolism. What carbon substrates can the genome likely use? Do you think it is respiratory e.g. using oxygen, nitrate, etc.? If not respiratory, what is evidence for fermentation? What other things are neat to note about this organism (use the metabolism_summary.xlsx or annotations.tsv)? Does it partake in H2 metabolism, CO2 fixation, or have any characteristics listed in the MISC tab (flagella, CRISPR)?

Annotate and Distill Assemblies with DRAM
Annotate your assemblies, isolate genomes, or MAGs with DRAM and distill resulting annotations to create an interactive functional summary per genome or assembly. Use for KBase assembly objects.
This app completed without errors in 1d 2h 17m 25s.
Objects
Created Object Name Type Description
CONGO_003_metagenome_DASTool.240717_bin.001.fasta_DRAM Genome Annotated Genome
CONGO_003_metagenome_DASTool.240717_bin.002.fasta_DRAM Genome Annotated Genome
CONGO_003_metagenome_DASTool.240717_bin.004.fasta_DRAM Genome Annotated Genome
CONGO_003_metagenome_DASTool.240717_bin.007.fasta_DRAM Genome Annotated Genome
CONGO_007_metagenome_DASTool.240722_bin.001.fasta_DRAM Genome Annotated Genome
CONGO_007_metagenome_DASTool.240722_bin.003.fasta_DRAM Genome Annotated Genome
CONGO_007_metagenome_DASTool.240722_bin.004.fasta_DRAM Genome Annotated Genome
CONGO_007_metagenome_DASTool.240722_bin.005.fasta_DRAM Genome Annotated Genome
CONGO_007_metagenome_DASTool.240722_bin.009.fasta_DRAM Genome Annotated Genome
CONGO_007_metagenome_DASTool.240722_bin.010.fasta_DRAM Genome Annotated Genome
CONGO_007_metagenome_DASTool.240722_bin.011.fasta_DRAM Genome Annotated Genome
CONGO_007_metagenome_DASTool.240722_bin.012.fasta_DRAM Genome Annotated Genome
CONGO_007_metagenome_DASTool.240722_bin.014.fasta_DRAM Genome Annotated Genome
CONGO_007_metagenome_DASTool.240722_bin.016.fasta_DRAM Genome Annotated Genome
CONGO_007_metagenome_DASTool.240722_bin.017.fasta_DRAM Genome Annotated Genome
CONGO_007_metagenome_DASTool.240722_bin.018.fasta_DRAM Genome Annotated Genome
CONGO_007_metagenome_DASTool.240722_bin.019.fasta_DRAM Genome Annotated Genome
CONGO_007_metagenome_DASTool.240722_bin.022.fasta_DRAM Genome Annotated Genome
CONGO_007_metagenome_DASTool.240722_bin.024.fasta_DRAM Genome Annotated Genome
CONGO_007_metagenome_DASTool.240722_bin.025.fasta_DRAM Genome Annotated Genome
CONGO_017_metagenome_DASTool.240722_bin.001.fasta_DRAM Genome Annotated Genome
CONGO_017_metagenome_DASTool.240722_bin.005.fasta_DRAM Genome Annotated Genome
CONGO_031_metagenome_DASTool.240722_bin.001.fasta_DRAM Genome Annotated Genome
CONGO_031_metagenome_DASTool.240722_bin.002.fasta_DRAM Genome Annotated Genome
CONGO_031_metagenome_DASTool.240722_bin.003.fasta_DRAM Genome Annotated Genome
CONGO_031_metagenome_DASTool.240722_bin.006.fasta_DRAM Genome Annotated Genome
CONGO_031_metagenome_DASTool.240722_bin.007.fasta_DRAM Genome Annotated Genome
CONGO_031_metagenome_DASTool.240722_bin.009.fasta_DRAM Genome Annotated Genome
CONGO_031_metagenome_DASTool.240722_bin.010.fasta_DRAM Genome Annotated Genome
CONGO_031_metagenome_DASTool.240722_bin.013.fasta_DRAM Genome Annotated Genome
CONGO_031_metagenome_DASTool.240722_bin.015.fasta_DRAM Genome Annotated Genome
CONGO_040_metagenome_DASTool.240722_bin.001.fasta_DRAM Genome Annotated Genome
CONGO_040_metagenome_DASTool.240722_bin.002.fasta_DRAM Genome Annotated Genome
CONGO_040_metagenome_DASTool.240722_bin.006.fasta_DRAM Genome Annotated Genome
CONGO_040_metagenome_DASTool.240722_bin.009.fasta_DRAM Genome Annotated Genome
CONGO_040_metagenome_DASTool.240722_bin.010.fasta_DRAM Genome Annotated Genome
CONGO_040_metagenome_DASTool.240722_bin.011.fasta_DRAM Genome Annotated Genome
CONGO_040_metagenome_DASTool.240722_bin.012.fasta_DRAM Genome Annotated Genome
CONGO_040_metagenome_DASTool.240722_bin.015.fasta_DRAM Genome Annotated Genome
CONGO_040_metagenome_DASTool.240722_bin.017.fasta_DRAM Genome Annotated Genome
CONGO_063_metagenome_DASTool.240722_bin.005.fasta_DRAM Genome Annotated Genome
CONGO_063_metagenome_DASTool.240722_bin.011.fasta_DRAM Genome Annotated Genome
CONGO_063_metagenome_DASTool.240722_bin.012.fasta_DRAM Genome Annotated Genome
CONGO_063_metagenome_DASTool.240722_bin.013.fasta_DRAM Genome Annotated Genome
CONGO_065_metagenome_DASTool.240722_bin.001.fasta_DRAM Genome Annotated Genome
CONGO_065_metagenome_DASTool.240722_bin.008.fasta_DRAM Genome Annotated Genome
CONGO_065_metagenome_DASTool.240722_bin.010.fasta_DRAM Genome Annotated Genome
CONGO_067_metagenome_DASTool.240722_bin.002.fasta_DRAM Genome Annotated Genome
CONGO_067_metagenome_DASTool.240722_bin.003.fasta_DRAM Genome Annotated Genome
CONGO_067_metagenome_DASTool.240722_bin.007.fasta_DRAM Genome Annotated Genome
CONGO_067_metagenome_DASTool.240722_bin.012.fasta_DRAM Genome Annotated Genome
CONGO_metagenomes_dRep_DRAM.240729 GenomeSet CONGO metagenome bins from dRep
Report
Summary
Here are the results from your DRAM run.
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/187935
  • annotations.tsv - DRAM annotations in a tab separate table format
  • genes.fna - Genes as nucleotides predicted by DRAM with brief annotations
  • genes.faa - Genes as amino acids predicted by DRAM with brief annotations
  • genes.gff - GFF file of all DRAM annotations
  • rrnas.tsv - Tab separated table of rRNAs as detected by barrnap
  • trnas.tsv - Tab separated table of tRNAs as detected by tRNAscan-SE
  • genbank.tar.gz - Compressed folder of output genbank files
  • product.tsv - DRAM product in tabular format
  • metabolism_summary.xlsx - DRAM metabolism summary tables
  • genome_stats.tsv - DRAM genome statistics table
Build GenomeSet - v1.7.6
Allows users to create a GenomeSet object.
This app completed without errors in 17s.
Objects
Created Object Name Type Description
CONGO_003_MAGs_dRep_DRAM.240801 GenomeSet KButil_Build_GenomeSet
Summary
genomes in output set CONGO_003_MAGs_dRep_DRAM.240801: 4
Classify Microbes with GTDB-Tk - v2.3.2
Obtain objective taxonomic assignments for bacterial and archaeal genomes based on the Genome Taxonomy Database (GTDB)
This app completed without errors in 23m 29s.
Objects
Created Object Name Type Description
CONGO_003_metagenome_DASTool.240717_bin.001.fasta_DRAM Genome Taxonomy and taxon_assignment updated with GTDB
CONGO_003_metagenome_DASTool.240717_bin.002.fasta_DRAM Genome Taxonomy and taxon_assignment updated with GTDB
CONGO_003_metagenome_DASTool.240717_bin.004.fasta_DRAM Genome Taxonomy and taxon_assignment updated with GTDB
CONGO_003_metagenome_DASTool.240717_bin.007.fasta_DRAM Genome Taxonomy and taxon_assignment updated with GTDB
CONGO_003_MAGs_dRep_DRAM.240801 GenomeSet Taxonomy and taxon_assignment updated with GTDB
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/187935
  • gtdbtk.backbone.bac120.classify.tree - gtdbtk.backbone.bac120.classify.tree - whole tree GTDB formatted Newick
  • gtdbtk.backbone.bac120.classify-ITOL.tree - gtdbtk.backbone.bac120.classify-ITOL.tree - whole tree ITOL formatted Newick
  • gtdbtk.bac120.classify.tree.1.tree - gtdbtk.bac120.classify.tree.1.tree - whole tree GTDB formatted Newick
  • gtdbtk.bac120.classify.tree.1-ITOL.tree - gtdbtk.bac120.classify.tree.1-ITOL.tree - whole tree ITOL formatted Newick
  • gtdbtk.backbone.bac120.classify-proximals.tree - gtdbtk.backbone.bac120.classify-proximals.tree - Newick
  • gtdbtk.backbone.bac120.classify-trimmed.tree - gtdbtk.backbone.bac120.classify-trimmed.tree - Newick
  • gtdbtk.backbone.bac120.classify-lineages.map - gtdbtk.backbone.bac120.classify-lineages.map - GTDB lineage
  • gtdbtk.backbone.bac120.classify-trimmed.tree-rectangle.PNG - gtdbtk.backbone.bac120.classify-trimmed.tree - Image
  • gtdbtk.backbone.bac120.classify-trimmed.tree-rectangle.PDF - gtdbtk.backbone.bac120.classify-trimmed.tree - Image
  • gtdbtk.backbone.bac120.classify-trimmed.tree-circle.PNG - gtdbtk.backbone.bac120.classify-trimmed.tree - Image
  • gtdbtk.backbone.bac120.classify-trimmed.tree-circle.PDF - gtdbtk.backbone.bac120.classify-trimmed.tree - Image
  • gtdbtk.backbone.bac120.classify-trimmed.tree-circle-ultrametric.PNG - gtdbtk.backbone.bac120.classify-trimmed.tree - Image
  • gtdbtk.backbone.bac120.classify-trimmed.tree-circle-ultrametric.PDF - gtdbtk.backbone.bac120.classify-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.1-proximals.tree - gtdbtk.bac120.classify.tree.1-proximals.tree - Newick
  • gtdbtk.bac120.classify.tree.1-trimmed.tree - gtdbtk.bac120.classify.tree.1-trimmed.tree - Newick
  • gtdbtk.bac120.classify.tree.1-lineages.map - gtdbtk.bac120.classify.tree.1-lineages.map - GTDB lineage
  • gtdbtk.bac120.classify.tree.1-trimmed.tree-rectangle.PNG - gtdbtk.bac120.classify.tree.1-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.1-trimmed.tree-rectangle.PDF - gtdbtk.bac120.classify.tree.1-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.1-trimmed.tree-circle.PNG - gtdbtk.bac120.classify.tree.1-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.1-trimmed.tree-circle.PDF - gtdbtk.bac120.classify.tree.1-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.1-trimmed.tree-circle-ultrametric.PNG - gtdbtk.bac120.classify.tree.1-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.1-trimmed.tree-circle-ultrametric.PDF - gtdbtk.bac120.classify.tree.1-trimmed.tree - Image
  • GTDB-Tk_classify_wf.zip - GTDB-Tk Classify WF output
Build GenomeSet - v1.7.6
Allows users to create a GenomeSet object.
This app completed without errors in 34s.
Objects
Created Object Name Type Description
CONGO_007_MAGs_dRep_DRAM.240801 GenomeSet KButil_Build_GenomeSet
Summary
genomes in output set CONGO_007_MAGs_dRep_DRAM.240801: 16
Classify Microbes with GTDB-Tk - v2.3.2
Obtain objective taxonomic assignments for bacterial and archaeal genomes based on the Genome Taxonomy Database (GTDB)
This app completed without errors in 56m 53s.
Objects
Created Object Name Type Description
CONGO_007_metagenome_DASTool.240722_bin.001.fasta_DRAM Genome Taxonomy unchanged, taxon_assignment added GTDB
CONGO_007_metagenome_DASTool.240722_bin.003.fasta_DRAM Genome Taxonomy unchanged, taxon_assignment added GTDB
CONGO_007_metagenome_DASTool.240722_bin.004.fasta_DRAM Genome Taxonomy unchanged, taxon_assignment added GTDB
CONGO_007_metagenome_DASTool.240722_bin.005.fasta_DRAM Genome Taxonomy unchanged, taxon_assignment added GTDB
CONGO_007_metagenome_DASTool.240722_bin.009.fasta_DRAM Genome Taxonomy unchanged, taxon_assignment added GTDB
CONGO_007_metagenome_DASTool.240722_bin.010.fasta_DRAM Genome Taxonomy unchanged, taxon_assignment added GTDB
CONGO_007_metagenome_DASTool.240722_bin.011.fasta_DRAM Genome Taxonomy unchanged, taxon_assignment added GTDB
CONGO_007_metagenome_DASTool.240722_bin.012.fasta_DRAM Genome Taxonomy unchanged, taxon_assignment added GTDB
CONGO_007_metagenome_DASTool.240722_bin.014.fasta_DRAM Genome Taxonomy unchanged, taxon_assignment added GTDB
CONGO_007_metagenome_DASTool.240722_bin.016.fasta_DRAM Genome Taxonomy unchanged, taxon_assignment added GTDB
CONGO_007_metagenome_DASTool.240722_bin.017.fasta_DRAM Genome Taxonomy unchanged, taxon_assignment added GTDB
CONGO_007_metagenome_DASTool.240722_bin.018.fasta_DRAM Genome Taxonomy unchanged, taxon_assignment added GTDB
CONGO_007_metagenome_DASTool.240722_bin.019.fasta_DRAM Genome Taxonomy unchanged, taxon_assignment added GTDB
CONGO_007_metagenome_DASTool.240722_bin.022.fasta_DRAM Genome Taxonomy unchanged, taxon_assignment added GTDB
CONGO_007_metagenome_DASTool.240722_bin.024.fasta_DRAM Genome Taxonomy unchanged, taxon_assignment added GTDB
CONGO_007_metagenome_DASTool.240722_bin.025.fasta_DRAM Genome Taxonomy unchanged, taxon_assignment added GTDB
CONGO_007_MAGs_dRep_DRAM.240801 GenomeSet Taxonomy and taxon_assignment updated with GTDB
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/187935
  • gtdbtk.backbone.bac120.classify.tree - gtdbtk.backbone.bac120.classify.tree - whole tree GTDB formatted Newick
  • gtdbtk.backbone.bac120.classify-ITOL.tree - gtdbtk.backbone.bac120.classify-ITOL.tree - whole tree ITOL formatted Newick
  • gtdbtk.bac120.classify.tree.1.tree - gtdbtk.bac120.classify.tree.1.tree - whole tree GTDB formatted Newick
  • gtdbtk.bac120.classify.tree.1-ITOL.tree - gtdbtk.bac120.classify.tree.1-ITOL.tree - whole tree ITOL formatted Newick
  • gtdbtk.bac120.classify.tree.4.tree - gtdbtk.bac120.classify.tree.4.tree - whole tree GTDB formatted Newick
  • gtdbtk.bac120.classify.tree.4-ITOL.tree - gtdbtk.bac120.classify.tree.4-ITOL.tree - whole tree ITOL formatted Newick
  • gtdbtk.bac120.classify.tree.5.tree - gtdbtk.bac120.classify.tree.5.tree - whole tree GTDB formatted Newick
  • gtdbtk.bac120.classify.tree.5-ITOL.tree - gtdbtk.bac120.classify.tree.5-ITOL.tree - whole tree ITOL formatted Newick
  • gtdbtk.bac120.classify.tree.8.tree - gtdbtk.bac120.classify.tree.8.tree - whole tree GTDB formatted Newick
  • gtdbtk.bac120.classify.tree.8-ITOL.tree - gtdbtk.bac120.classify.tree.8-ITOL.tree - whole tree ITOL formatted Newick
  • gtdbtk.backbone.bac120.classify-proximals.tree - gtdbtk.backbone.bac120.classify-proximals.tree - Newick
  • gtdbtk.backbone.bac120.classify-trimmed.tree - gtdbtk.backbone.bac120.classify-trimmed.tree - Newick
  • gtdbtk.backbone.bac120.classify-lineages.map - gtdbtk.backbone.bac120.classify-lineages.map - GTDB lineage
  • gtdbtk.backbone.bac120.classify-trimmed.tree-rectangle.PNG - gtdbtk.backbone.bac120.classify-trimmed.tree - Image
  • gtdbtk.backbone.bac120.classify-trimmed.tree-rectangle.PDF - gtdbtk.backbone.bac120.classify-trimmed.tree - Image
  • gtdbtk.backbone.bac120.classify-trimmed.tree-circle.PNG - gtdbtk.backbone.bac120.classify-trimmed.tree - Image
  • gtdbtk.backbone.bac120.classify-trimmed.tree-circle.PDF - gtdbtk.backbone.bac120.classify-trimmed.tree - Image
  • gtdbtk.backbone.bac120.classify-trimmed.tree-circle-ultrametric.PNG - gtdbtk.backbone.bac120.classify-trimmed.tree - Image
  • gtdbtk.backbone.bac120.classify-trimmed.tree-circle-ultrametric.PDF - gtdbtk.backbone.bac120.classify-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.1-proximals.tree - gtdbtk.bac120.classify.tree.1-proximals.tree - Newick
  • gtdbtk.bac120.classify.tree.1-trimmed.tree - gtdbtk.bac120.classify.tree.1-trimmed.tree - Newick
  • gtdbtk.bac120.classify.tree.1-lineages.map - gtdbtk.bac120.classify.tree.1-lineages.map - GTDB lineage
  • gtdbtk.bac120.classify.tree.1-trimmed.tree-rectangle.PNG - gtdbtk.bac120.classify.tree.1-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.1-trimmed.tree-rectangle.PDF - gtdbtk.bac120.classify.tree.1-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.1-trimmed.tree-circle.PNG - gtdbtk.bac120.classify.tree.1-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.1-trimmed.tree-circle.PDF - gtdbtk.bac120.classify.tree.1-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.1-trimmed.tree-circle-ultrametric.PNG - gtdbtk.bac120.classify.tree.1-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.1-trimmed.tree-circle-ultrametric.PDF - gtdbtk.bac120.classify.tree.1-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.4-proximals.tree - gtdbtk.bac120.classify.tree.4-proximals.tree - Newick
  • gtdbtk.bac120.classify.tree.4-trimmed.tree - gtdbtk.bac120.classify.tree.4-trimmed.tree - Newick
  • gtdbtk.bac120.classify.tree.4-lineages.map - gtdbtk.bac120.classify.tree.4-lineages.map - GTDB lineage
  • gtdbtk.bac120.classify.tree.4-trimmed.tree-rectangle.PNG - gtdbtk.bac120.classify.tree.4-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.4-trimmed.tree-rectangle.PDF - gtdbtk.bac120.classify.tree.4-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.4-trimmed.tree-circle.PNG - gtdbtk.bac120.classify.tree.4-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.4-trimmed.tree-circle.PDF - gtdbtk.bac120.classify.tree.4-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.4-trimmed.tree-circle-ultrametric.PNG - gtdbtk.bac120.classify.tree.4-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.4-trimmed.tree-circle-ultrametric.PDF - gtdbtk.bac120.classify.tree.4-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.5-proximals.tree - gtdbtk.bac120.classify.tree.5-proximals.tree - Newick
  • gtdbtk.bac120.classify.tree.5-trimmed.tree - gtdbtk.bac120.classify.tree.5-trimmed.tree - Newick
  • gtdbtk.bac120.classify.tree.5-lineages.map - gtdbtk.bac120.classify.tree.5-lineages.map - GTDB lineage
  • gtdbtk.bac120.classify.tree.5-trimmed.tree-rectangle.PNG - gtdbtk.bac120.classify.tree.5-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.5-trimmed.tree-rectangle.PDF - gtdbtk.bac120.classify.tree.5-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.5-trimmed.tree-circle.PNG - gtdbtk.bac120.classify.tree.5-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.5-trimmed.tree-circle.PDF - gtdbtk.bac120.classify.tree.5-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.5-trimmed.tree-circle-ultrametric.PNG - gtdbtk.bac120.classify.tree.5-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.5-trimmed.tree-circle-ultrametric.PDF - gtdbtk.bac120.classify.tree.5-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.8-proximals.tree - gtdbtk.bac120.classify.tree.8-proximals.tree - Newick
  • gtdbtk.bac120.classify.tree.8-trimmed.tree - gtdbtk.bac120.classify.tree.8-trimmed.tree - Newick
  • gtdbtk.bac120.classify.tree.8-lineages.map - gtdbtk.bac120.classify.tree.8-lineages.map - GTDB lineage
  • gtdbtk.bac120.classify.tree.8-trimmed.tree-rectangle.PNG - gtdbtk.bac120.classify.tree.8-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.8-trimmed.tree-rectangle.PDF - gtdbtk.bac120.classify.tree.8-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.8-trimmed.tree-circle.PNG - gtdbtk.bac120.classify.tree.8-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.8-trimmed.tree-circle.PDF - gtdbtk.bac120.classify.tree.8-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.8-trimmed.tree-circle-ultrametric.PNG - gtdbtk.bac120.classify.tree.8-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.8-trimmed.tree-circle-ultrametric.PDF - gtdbtk.bac120.classify.tree.8-trimmed.tree - Image
  • GTDB-Tk_classify_wf.zip - GTDB-Tk Classify WF output
Build GenomeSet - v1.7.6
Allows users to create a GenomeSet object.
This app completed without errors in 16s.
Objects
Created Object Name Type Description
CONGO_017_MAGs_dRep_DRAM.240801 GenomeSet KButil_Build_GenomeSet
Summary
genomes in output set CONGO_017_MAGs_dRep_DRAM.240801: 2
Classify Microbes with GTDB-Tk - v2.3.2
Obtain objective taxonomic assignments for bacterial and archaeal genomes based on the Genome Taxonomy Database (GTDB)
This app completed without errors in 22m 13s.
Objects
Created Object Name Type Description
CONGO_017_metagenome_DASTool.240722_bin.001.fasta_DRAM Genome Taxonomy and taxon_assignment updated with GTDB
CONGO_017_metagenome_DASTool.240722_bin.005.fasta_DRAM Genome Taxonomy and taxon_assignment updated with GTDB
CONGO_017_MAGs_dRep_DRAM.240801 GenomeSet Taxonomy and taxon_assignment updated with GTDB
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/187935
  • gtdbtk.backbone.bac120.classify.tree - gtdbtk.backbone.bac120.classify.tree - whole tree GTDB formatted Newick
  • gtdbtk.backbone.bac120.classify-ITOL.tree - gtdbtk.backbone.bac120.classify-ITOL.tree - whole tree ITOL formatted Newick
  • gtdbtk.bac120.classify.tree.1.tree - gtdbtk.bac120.classify.tree.1.tree - whole tree GTDB formatted Newick
  • gtdbtk.bac120.classify.tree.1-ITOL.tree - gtdbtk.bac120.classify.tree.1-ITOL.tree - whole tree ITOL formatted Newick
  • gtdbtk.backbone.bac120.classify-proximals.tree - gtdbtk.backbone.bac120.classify-proximals.tree - Newick
  • gtdbtk.backbone.bac120.classify-trimmed.tree - gtdbtk.backbone.bac120.classify-trimmed.tree - Newick
  • gtdbtk.backbone.bac120.classify-lineages.map - gtdbtk.backbone.bac120.classify-lineages.map - GTDB lineage
  • gtdbtk.backbone.bac120.classify-trimmed.tree-rectangle.PNG - gtdbtk.backbone.bac120.classify-trimmed.tree - Image
  • gtdbtk.backbone.bac120.classify-trimmed.tree-rectangle.PDF - gtdbtk.backbone.bac120.classify-trimmed.tree - Image
  • gtdbtk.backbone.bac120.classify-trimmed.tree-circle.PNG - gtdbtk.backbone.bac120.classify-trimmed.tree - Image
  • gtdbtk.backbone.bac120.classify-trimmed.tree-circle.PDF - gtdbtk.backbone.bac120.classify-trimmed.tree - Image
  • gtdbtk.backbone.bac120.classify-trimmed.tree-circle-ultrametric.PNG - gtdbtk.backbone.bac120.classify-trimmed.tree - Image
  • gtdbtk.backbone.bac120.classify-trimmed.tree-circle-ultrametric.PDF - gtdbtk.backbone.bac120.classify-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.1-proximals.tree - gtdbtk.bac120.classify.tree.1-proximals.tree - Newick
  • gtdbtk.bac120.classify.tree.1-trimmed.tree - gtdbtk.bac120.classify.tree.1-trimmed.tree - Newick
  • gtdbtk.bac120.classify.tree.1-lineages.map - gtdbtk.bac120.classify.tree.1-lineages.map - GTDB lineage
  • gtdbtk.bac120.classify.tree.1-trimmed.tree-rectangle.PNG - gtdbtk.bac120.classify.tree.1-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.1-trimmed.tree-rectangle.PDF - gtdbtk.bac120.classify.tree.1-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.1-trimmed.tree-circle.PNG - gtdbtk.bac120.classify.tree.1-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.1-trimmed.tree-circle.PDF - gtdbtk.bac120.classify.tree.1-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.1-trimmed.tree-circle-ultrametric.PNG - gtdbtk.bac120.classify.tree.1-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.1-trimmed.tree-circle-ultrametric.PDF - gtdbtk.bac120.classify.tree.1-trimmed.tree - Image
  • GTDB-Tk_classify_wf.zip - GTDB-Tk Classify WF output
Build GenomeSet - v1.7.6
Allows users to create a GenomeSet object.
This app completed without errors in 33s.
Objects
Created Object Name Type Description
CONGO_031_MAGs_dRep_DRAM.240801 GenomeSet KButil_Build_GenomeSet
Summary
genomes in output set CONGO_031_MAGs_dRep_DRAM.240801: 9
Classify Microbes with GTDB-Tk - v2.3.2
Obtain objective taxonomic assignments for bacterial and archaeal genomes based on the Genome Taxonomy Database (GTDB)
This app completed without errors in 1h 7m 52s.
Objects
Created Object Name Type Description
CONGO_031_metagenome_DASTool.240722_bin.001.fasta_DRAM Genome Taxonomy and taxon_assignment updated with GTDB
CONGO_031_metagenome_DASTool.240722_bin.002.fasta_DRAM Genome Taxonomy and taxon_assignment updated with GTDB
CONGO_031_metagenome_DASTool.240722_bin.003.fasta_DRAM Genome Taxonomy and taxon_assignment updated with GTDB
CONGO_031_metagenome_DASTool.240722_bin.006.fasta_DRAM Genome Taxonomy and taxon_assignment updated with GTDB
CONGO_031_metagenome_DASTool.240722_bin.007.fasta_DRAM Genome Taxonomy unchanged, taxon_assignment added GTDB
CONGO_031_metagenome_DASTool.240722_bin.009.fasta_DRAM Genome Taxonomy unchanged, taxon_assignment added GTDB
CONGO_031_metagenome_DASTool.240722_bin.010.fasta_DRAM Genome Taxonomy unchanged, taxon_assignment added GTDB
CONGO_031_metagenome_DASTool.240722_bin.013.fasta_DRAM Genome Taxonomy unchanged, taxon_assignment added GTDB
CONGO_031_metagenome_DASTool.240722_bin.015.fasta_DRAM Genome Taxonomy unchanged, taxon_assignment added GTDB
CONGO_031_MAGs_dRep_DRAM.240801 GenomeSet Taxonomy and taxon_assignment updated with GTDB
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/187935
  • gtdbtk.backbone.bac120.classify.tree - gtdbtk.backbone.bac120.classify.tree - whole tree GTDB formatted Newick
  • gtdbtk.backbone.bac120.classify-ITOL.tree - gtdbtk.backbone.bac120.classify-ITOL.tree - whole tree ITOL formatted Newick
  • gtdbtk.bac120.classify.tree.1.tree - gtdbtk.bac120.classify.tree.1.tree - whole tree GTDB formatted Newick
  • gtdbtk.bac120.classify.tree.1-ITOL.tree - gtdbtk.bac120.classify.tree.1-ITOL.tree - whole tree ITOL formatted Newick
  • gtdbtk.bac120.classify.tree.3.tree - gtdbtk.bac120.classify.tree.3.tree - whole tree GTDB formatted Newick
  • gtdbtk.bac120.classify.tree.3-ITOL.tree - gtdbtk.bac120.classify.tree.3-ITOL.tree - whole tree ITOL formatted Newick
  • gtdbtk.bac120.classify.tree.5.tree - gtdbtk.bac120.classify.tree.5.tree - whole tree GTDB formatted Newick
  • gtdbtk.bac120.classify.tree.5-ITOL.tree - gtdbtk.bac120.classify.tree.5-ITOL.tree - whole tree ITOL formatted Newick
  • gtdbtk.backbone.bac120.classify-proximals.tree - gtdbtk.backbone.bac120.classify-proximals.tree - Newick
  • gtdbtk.backbone.bac120.classify-trimmed.tree - gtdbtk.backbone.bac120.classify-trimmed.tree - Newick
  • gtdbtk.backbone.bac120.classify-lineages.map - gtdbtk.backbone.bac120.classify-lineages.map - GTDB lineage
  • gtdbtk.backbone.bac120.classify-trimmed.tree-rectangle.PNG - gtdbtk.backbone.bac120.classify-trimmed.tree - Image
  • gtdbtk.backbone.bac120.classify-trimmed.tree-rectangle.PDF - gtdbtk.backbone.bac120.classify-trimmed.tree - Image
  • gtdbtk.backbone.bac120.classify-trimmed.tree-circle.PNG - gtdbtk.backbone.bac120.classify-trimmed.tree - Image
  • gtdbtk.backbone.bac120.classify-trimmed.tree-circle.PDF - gtdbtk.backbone.bac120.classify-trimmed.tree - Image
  • gtdbtk.backbone.bac120.classify-trimmed.tree-circle-ultrametric.PNG - gtdbtk.backbone.bac120.classify-trimmed.tree - Image
  • gtdbtk.backbone.bac120.classify-trimmed.tree-circle-ultrametric.PDF - gtdbtk.backbone.bac120.classify-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.1-proximals.tree - gtdbtk.bac120.classify.tree.1-proximals.tree - Newick
  • gtdbtk.bac120.classify.tree.1-trimmed.tree - gtdbtk.bac120.classify.tree.1-trimmed.tree - Newick
  • gtdbtk.bac120.classify.tree.1-lineages.map - gtdbtk.bac120.classify.tree.1-lineages.map - GTDB lineage
  • gtdbtk.bac120.classify.tree.1-trimmed.tree-rectangle.PNG - gtdbtk.bac120.classify.tree.1-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.1-trimmed.tree-rectangle.PDF - gtdbtk.bac120.classify.tree.1-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.1-trimmed.tree-circle.PNG - gtdbtk.bac120.classify.tree.1-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.1-trimmed.tree-circle.PDF - gtdbtk.bac120.classify.tree.1-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.1-trimmed.tree-circle-ultrametric.PNG - gtdbtk.bac120.classify.tree.1-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.1-trimmed.tree-circle-ultrametric.PDF - gtdbtk.bac120.classify.tree.1-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.3-proximals.tree - gtdbtk.bac120.classify.tree.3-proximals.tree - Newick
  • gtdbtk.bac120.classify.tree.3-trimmed.tree - gtdbtk.bac120.classify.tree.3-trimmed.tree - Newick
  • gtdbtk.bac120.classify.tree.3-lineages.map - gtdbtk.bac120.classify.tree.3-lineages.map - GTDB lineage
  • gtdbtk.bac120.classify.tree.3-trimmed.tree-rectangle.PNG - gtdbtk.bac120.classify.tree.3-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.3-trimmed.tree-rectangle.PDF - gtdbtk.bac120.classify.tree.3-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.3-trimmed.tree-circle.PNG - gtdbtk.bac120.classify.tree.3-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.3-trimmed.tree-circle.PDF - gtdbtk.bac120.classify.tree.3-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.3-trimmed.tree-circle-ultrametric.PNG - gtdbtk.bac120.classify.tree.3-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.3-trimmed.tree-circle-ultrametric.PDF - gtdbtk.bac120.classify.tree.3-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.5-proximals.tree - gtdbtk.bac120.classify.tree.5-proximals.tree - Newick
  • gtdbtk.bac120.classify.tree.5-trimmed.tree - gtdbtk.bac120.classify.tree.5-trimmed.tree - Newick
  • gtdbtk.bac120.classify.tree.5-lineages.map - gtdbtk.bac120.classify.tree.5-lineages.map - GTDB lineage
  • gtdbtk.bac120.classify.tree.5-trimmed.tree-rectangle.PNG - gtdbtk.bac120.classify.tree.5-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.5-trimmed.tree-rectangle.PDF - gtdbtk.bac120.classify.tree.5-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.5-trimmed.tree-circle.PNG - gtdbtk.bac120.classify.tree.5-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.5-trimmed.tree-circle.PDF - gtdbtk.bac120.classify.tree.5-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.5-trimmed.tree-circle-ultrametric.PNG - gtdbtk.bac120.classify.tree.5-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.5-trimmed.tree-circle-ultrametric.PDF - gtdbtk.bac120.classify.tree.5-trimmed.tree - Image
  • GTDB-Tk_classify_wf.zip - GTDB-Tk Classify WF output
Build GenomeSet - v1.7.6
Allows users to create a GenomeSet object.
This app completed without errors in 27s.
Objects
Created Object Name Type Description
CONGO_040_MAGs_dRep_DRAM.240801 GenomeSet KButil_Build_GenomeSet
Summary
genomes in output set CONGO_040_MAGs_dRep_DRAM.240801: 9
Classify Microbes with GTDB-Tk - v2.3.2
Obtain objective taxonomic assignments for bacterial and archaeal genomes based on the Genome Taxonomy Database (GTDB)
This app completed without errors in 54m 34s.
Objects
Created Object Name Type Description
CONGO_040_metagenome_DASTool.240722_bin.010.fasta_DRAM Genome Taxonomy and taxon_assignment updated with GTDB
CONGO_040_metagenome_DASTool.240722_bin.011.fasta_DRAM Genome Taxonomy and taxon_assignment updated with GTDB
CONGO_040_metagenome_DASTool.240722_bin.012.fasta_DRAM Genome Taxonomy and taxon_assignment updated with GTDB
CONGO_040_metagenome_DASTool.240722_bin.015.fasta_DRAM Genome Taxonomy and taxon_assignment updated with GTDB
CONGO_040_metagenome_DASTool.240722_bin.017.fasta_DRAM Genome Taxonomy and taxon_assignment updated with GTDB
CONGO_040_metagenome_DASTool.240722_bin.001.fasta_DRAM Genome Taxonomy and taxon_assignment updated with GTDB
CONGO_040_metagenome_DASTool.240722_bin.002.fasta_DRAM Genome Taxonomy and taxon_assignment updated with GTDB
CONGO_040_metagenome_DASTool.240722_bin.006.fasta_DRAM Genome Taxonomy and taxon_assignment updated with GTDB
CONGO_040_metagenome_DASTool.240722_bin.009.fasta_DRAM Genome Taxonomy and taxon_assignment updated with GTDB
CONGO_040_MAGs_dRep_DRAM.240801 GenomeSet Taxonomy and taxon_assignment updated with GTDB
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/187935
  • gtdbtk.backbone.bac120.classify.tree - gtdbtk.backbone.bac120.classify.tree - whole tree GTDB formatted Newick
  • gtdbtk.backbone.bac120.classify-ITOL.tree - gtdbtk.backbone.bac120.classify-ITOL.tree - whole tree ITOL formatted Newick
  • gtdbtk.bac120.classify.tree.1.tree - gtdbtk.bac120.classify.tree.1.tree - whole tree GTDB formatted Newick
  • gtdbtk.bac120.classify.tree.1-ITOL.tree - gtdbtk.bac120.classify.tree.1-ITOL.tree - whole tree ITOL formatted Newick
  • gtdbtk.bac120.classify.tree.4.tree - gtdbtk.bac120.classify.tree.4.tree - whole tree GTDB formatted Newick
  • gtdbtk.bac120.classify.tree.4-ITOL.tree - gtdbtk.bac120.classify.tree.4-ITOL.tree - whole tree ITOL formatted Newick
  • gtdbtk.bac120.classify.tree.5.tree - gtdbtk.bac120.classify.tree.5.tree - whole tree GTDB formatted Newick
  • gtdbtk.bac120.classify.tree.5-ITOL.tree - gtdbtk.bac120.classify.tree.5-ITOL.tree - whole tree ITOL formatted Newick
  • gtdbtk.bac120.classify.tree.8.tree - gtdbtk.bac120.classify.tree.8.tree - whole tree GTDB formatted Newick
  • gtdbtk.bac120.classify.tree.8-ITOL.tree - gtdbtk.bac120.classify.tree.8-ITOL.tree - whole tree ITOL formatted Newick
  • gtdbtk.backbone.bac120.classify-proximals.tree - gtdbtk.backbone.bac120.classify-proximals.tree - Newick
  • gtdbtk.backbone.bac120.classify-trimmed.tree - gtdbtk.backbone.bac120.classify-trimmed.tree - Newick
  • gtdbtk.backbone.bac120.classify-lineages.map - gtdbtk.backbone.bac120.classify-lineages.map - GTDB lineage
  • gtdbtk.backbone.bac120.classify-trimmed.tree-rectangle.PNG - gtdbtk.backbone.bac120.classify-trimmed.tree - Image
  • gtdbtk.backbone.bac120.classify-trimmed.tree-rectangle.PDF - gtdbtk.backbone.bac120.classify-trimmed.tree - Image
  • gtdbtk.backbone.bac120.classify-trimmed.tree-circle.PNG - gtdbtk.backbone.bac120.classify-trimmed.tree - Image
  • gtdbtk.backbone.bac120.classify-trimmed.tree-circle.PDF - gtdbtk.backbone.bac120.classify-trimmed.tree - Image
  • gtdbtk.backbone.bac120.classify-trimmed.tree-circle-ultrametric.PNG - gtdbtk.backbone.bac120.classify-trimmed.tree - Image
  • gtdbtk.backbone.bac120.classify-trimmed.tree-circle-ultrametric.PDF - gtdbtk.backbone.bac120.classify-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.1-proximals.tree - gtdbtk.bac120.classify.tree.1-proximals.tree - Newick
  • gtdbtk.bac120.classify.tree.1-trimmed.tree - gtdbtk.bac120.classify.tree.1-trimmed.tree - Newick
  • gtdbtk.bac120.classify.tree.1-lineages.map - gtdbtk.bac120.classify.tree.1-lineages.map - GTDB lineage
  • gtdbtk.bac120.classify.tree.1-trimmed.tree-rectangle.PNG - gtdbtk.bac120.classify.tree.1-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.1-trimmed.tree-rectangle.PDF - gtdbtk.bac120.classify.tree.1-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.1-trimmed.tree-circle.PNG - gtdbtk.bac120.classify.tree.1-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.1-trimmed.tree-circle.PDF - gtdbtk.bac120.classify.tree.1-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.1-trimmed.tree-circle-ultrametric.PNG - gtdbtk.bac120.classify.tree.1-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.1-trimmed.tree-circle-ultrametric.PDF - gtdbtk.bac120.classify.tree.1-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.4-proximals.tree - gtdbtk.bac120.classify.tree.4-proximals.tree - Newick
  • gtdbtk.bac120.classify.tree.4-trimmed.tree - gtdbtk.bac120.classify.tree.4-trimmed.tree - Newick
  • gtdbtk.bac120.classify.tree.4-lineages.map - gtdbtk.bac120.classify.tree.4-lineages.map - GTDB lineage
  • gtdbtk.bac120.classify.tree.4-trimmed.tree-rectangle.PNG - gtdbtk.bac120.classify.tree.4-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.4-trimmed.tree-rectangle.PDF - gtdbtk.bac120.classify.tree.4-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.4-trimmed.tree-circle.PNG - gtdbtk.bac120.classify.tree.4-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.4-trimmed.tree-circle.PDF - gtdbtk.bac120.classify.tree.4-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.4-trimmed.tree-circle-ultrametric.PNG - gtdbtk.bac120.classify.tree.4-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.4-trimmed.tree-circle-ultrametric.PDF - gtdbtk.bac120.classify.tree.4-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.5-proximals.tree - gtdbtk.bac120.classify.tree.5-proximals.tree - Newick
  • gtdbtk.bac120.classify.tree.5-trimmed.tree - gtdbtk.bac120.classify.tree.5-trimmed.tree - Newick
  • gtdbtk.bac120.classify.tree.5-lineages.map - gtdbtk.bac120.classify.tree.5-lineages.map - GTDB lineage
  • gtdbtk.bac120.classify.tree.5-trimmed.tree-rectangle.PNG - gtdbtk.bac120.classify.tree.5-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.5-trimmed.tree-rectangle.PDF - gtdbtk.bac120.classify.tree.5-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.5-trimmed.tree-circle.PNG - gtdbtk.bac120.classify.tree.5-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.5-trimmed.tree-circle.PDF - gtdbtk.bac120.classify.tree.5-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.5-trimmed.tree-circle-ultrametric.PNG - gtdbtk.bac120.classify.tree.5-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.5-trimmed.tree-circle-ultrametric.PDF - gtdbtk.bac120.classify.tree.5-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.8-proximals.tree - gtdbtk.bac120.classify.tree.8-proximals.tree - Newick
  • gtdbtk.bac120.classify.tree.8-trimmed.tree - gtdbtk.bac120.classify.tree.8-trimmed.tree - Newick
  • gtdbtk.bac120.classify.tree.8-lineages.map - gtdbtk.bac120.classify.tree.8-lineages.map - GTDB lineage
  • gtdbtk.bac120.classify.tree.8-trimmed.tree-rectangle.PNG - gtdbtk.bac120.classify.tree.8-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.8-trimmed.tree-rectangle.PDF - gtdbtk.bac120.classify.tree.8-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.8-trimmed.tree-circle.PNG - gtdbtk.bac120.classify.tree.8-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.8-trimmed.tree-circle.PDF - gtdbtk.bac120.classify.tree.8-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.8-trimmed.tree-circle-ultrametric.PNG - gtdbtk.bac120.classify.tree.8-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.8-trimmed.tree-circle-ultrametric.PDF - gtdbtk.bac120.classify.tree.8-trimmed.tree - Image
  • GTDB-Tk_classify_wf.zip - GTDB-Tk Classify WF output
Build GenomeSet - v1.7.6
Allows users to create a GenomeSet object.
This app completed without errors in 21s.
Objects
Created Object Name Type Description
CONGO_063_MAGs_dRep_DRAM.240801 GenomeSet KButil_Build_GenomeSet
Summary
genomes in output set CONGO_063_MAGs_dRep_DRAM.240801: 4
Classify Microbes with GTDB-Tk - v2.3.2
Obtain objective taxonomic assignments for bacterial and archaeal genomes based on the Genome Taxonomy Database (GTDB)
This app completed without errors in 37m 7s.
Objects
Created Object Name Type Description
CONGO_063_metagenome_DASTool.240722_bin.005.fasta_DRAM Genome Taxonomy and taxon_assignment updated with GTDB
CONGO_063_metagenome_DASTool.240722_bin.011.fasta_DRAM Genome Taxonomy and taxon_assignment updated with GTDB
CONGO_063_metagenome_DASTool.240722_bin.012.fasta_DRAM Genome Taxonomy and taxon_assignment updated with GTDB
CONGO_063_metagenome_DASTool.240722_bin.013.fasta_DRAM Genome Taxonomy and taxon_assignment updated with GTDB
CONGO_063_MAGs_dRep_DRAM.240801 GenomeSet Taxonomy and taxon_assignment updated with GTDB
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/187935
  • gtdbtk.backbone.bac120.classify.tree - gtdbtk.backbone.bac120.classify.tree - whole tree GTDB formatted Newick
  • gtdbtk.backbone.bac120.classify-ITOL.tree - gtdbtk.backbone.bac120.classify-ITOL.tree - whole tree ITOL formatted Newick
  • gtdbtk.bac120.classify.tree.1.tree - gtdbtk.bac120.classify.tree.1.tree - whole tree GTDB formatted Newick
  • gtdbtk.bac120.classify.tree.1-ITOL.tree - gtdbtk.bac120.classify.tree.1-ITOL.tree - whole tree ITOL formatted Newick
  • gtdbtk.bac120.classify.tree.5.tree - gtdbtk.bac120.classify.tree.5.tree - whole tree GTDB formatted Newick
  • gtdbtk.bac120.classify.tree.5-ITOL.tree - gtdbtk.bac120.classify.tree.5-ITOL.tree - whole tree ITOL formatted Newick
  • gtdbtk.bac120.classify.tree.8.tree - gtdbtk.bac120.classify.tree.8.tree - whole tree GTDB formatted Newick
  • gtdbtk.bac120.classify.tree.8-ITOL.tree - gtdbtk.bac120.classify.tree.8-ITOL.tree - whole tree ITOL formatted Newick
  • gtdbtk.backbone.bac120.classify-proximals.tree - gtdbtk.backbone.bac120.classify-proximals.tree - Newick
  • gtdbtk.backbone.bac120.classify-trimmed.tree - gtdbtk.backbone.bac120.classify-trimmed.tree - Newick
  • gtdbtk.backbone.bac120.classify-lineages.map - gtdbtk.backbone.bac120.classify-lineages.map - GTDB lineage
  • gtdbtk.backbone.bac120.classify-trimmed.tree-rectangle.PNG - gtdbtk.backbone.bac120.classify-trimmed.tree - Image
  • gtdbtk.backbone.bac120.classify-trimmed.tree-rectangle.PDF - gtdbtk.backbone.bac120.classify-trimmed.tree - Image
  • gtdbtk.backbone.bac120.classify-trimmed.tree-circle.PNG - gtdbtk.backbone.bac120.classify-trimmed.tree - Image
  • gtdbtk.backbone.bac120.classify-trimmed.tree-circle.PDF - gtdbtk.backbone.bac120.classify-trimmed.tree - Image
  • gtdbtk.backbone.bac120.classify-trimmed.tree-circle-ultrametric.PNG - gtdbtk.backbone.bac120.classify-trimmed.tree - Image
  • gtdbtk.backbone.bac120.classify-trimmed.tree-circle-ultrametric.PDF - gtdbtk.backbone.bac120.classify-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.1-proximals.tree - gtdbtk.bac120.classify.tree.1-proximals.tree - Newick
  • gtdbtk.bac120.classify.tree.1-trimmed.tree - gtdbtk.bac120.classify.tree.1-trimmed.tree - Newick
  • gtdbtk.bac120.classify.tree.1-lineages.map - gtdbtk.bac120.classify.tree.1-lineages.map - GTDB lineage
  • gtdbtk.bac120.classify.tree.1-trimmed.tree-rectangle.PNG - gtdbtk.bac120.classify.tree.1-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.1-trimmed.tree-rectangle.PDF - gtdbtk.bac120.classify.tree.1-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.1-trimmed.tree-circle.PNG - gtdbtk.bac120.classify.tree.1-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.1-trimmed.tree-circle.PDF - gtdbtk.bac120.classify.tree.1-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.1-trimmed.tree-circle-ultrametric.PNG - gtdbtk.bac120.classify.tree.1-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.1-trimmed.tree-circle-ultrametric.PDF - gtdbtk.bac120.classify.tree.1-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.5-proximals.tree - gtdbtk.bac120.classify.tree.5-proximals.tree - Newick
  • gtdbtk.bac120.classify.tree.5-trimmed.tree - gtdbtk.bac120.classify.tree.5-trimmed.tree - Newick
  • gtdbtk.bac120.classify.tree.5-lineages.map - gtdbtk.bac120.classify.tree.5-lineages.map - GTDB lineage
  • gtdbtk.bac120.classify.tree.5-trimmed.tree-rectangle.PNG - gtdbtk.bac120.classify.tree.5-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.5-trimmed.tree-rectangle.PDF - gtdbtk.bac120.classify.tree.5-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.5-trimmed.tree-circle.PNG - gtdbtk.bac120.classify.tree.5-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.5-trimmed.tree-circle.PDF - gtdbtk.bac120.classify.tree.5-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.5-trimmed.tree-circle-ultrametric.PNG - gtdbtk.bac120.classify.tree.5-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.5-trimmed.tree-circle-ultrametric.PDF - gtdbtk.bac120.classify.tree.5-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.8-proximals.tree - gtdbtk.bac120.classify.tree.8-proximals.tree - Newick
  • gtdbtk.bac120.classify.tree.8-trimmed.tree - gtdbtk.bac120.classify.tree.8-trimmed.tree - Newick
  • gtdbtk.bac120.classify.tree.8-lineages.map - gtdbtk.bac120.classify.tree.8-lineages.map - GTDB lineage
  • gtdbtk.bac120.classify.tree.8-trimmed.tree-rectangle.PNG - gtdbtk.bac120.classify.tree.8-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.8-trimmed.tree-rectangle.PDF - gtdbtk.bac120.classify.tree.8-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.8-trimmed.tree-circle.PNG - gtdbtk.bac120.classify.tree.8-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.8-trimmed.tree-circle.PDF - gtdbtk.bac120.classify.tree.8-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.8-trimmed.tree-circle-ultrametric.PNG - gtdbtk.bac120.classify.tree.8-trimmed.tree - Image
  • gtdbtk.bac120.classify.tree.8-trimmed.tree-circle-ultrametric.PDF - gtdbtk.bac120.classify.tree.8-trimmed.tree - Image
  • GTDB-Tk_classify_wf.zip - GTDB-Tk Classify WF output
Classify Microbes with GTDB-Tk - v1.7.0
Obtain objective taxonomic assignments for bacterial and archaeal genomes based on the Genome Taxonomy Database (GTDB) ver R06-RS202
This app completed without errors in 51m 26s.
Report
Links

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Apps in Beta

  1. Classify Microbes with GTDB-Tk - v1.7.0
    • Pierre-Alain Chaumeil, Aaron J Mussig, Philip Hugenholtz, Donovan H Parks, GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database, Bioinformatics, Volume 36, Issue 6, 15 March 2020, Pages 1925 1927. DOI: https://doi.org/10.1093/bioinformatics/btz848
    • Parks, D., Chuvochina, M., Waite, D. et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol 36, 996 1004 (2018). DOI: https://doi.org/10.1038/nbt.4229
    • Parks DH, Chuvochina M, Chaumeil PA, Rinke C, Mussig AJ, Hugenholtz P. A complete domain-to-species taxonomy for Bacteria and Archaea. Nat Biotechnol. 2020;10.1038/s41587-020-0501-8. DOI:10.1038/s41587-020-0501-8
    • Rinke C, Chuvochina M, Mussig AJ, Chaumeil PA, Dav n AA, Waite DW, Whitman WB, Parks DH, and Hugenholtz P. A standardized archaeal taxonomy for the Genome Taxonomy Database. Nat Microbiol. 2021 Jul;6(7):946-959. DOI:10.1038/s41564-021-00918-8
    • Matsen FA, Kodner RB, Armbrust EV. pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinformatics. 2010;11:538. Published 2010 Oct 30. doi:10.1186/1471-2105-11-538
    • Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun. 2018;9(1):5114. Published 2018 Nov 30. DOI:10.1038/s41467-018-07641-9
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