# Welcome to the Narrative
from IPython.display import IFrame
IFrame("https://www.kbase.us/narrative-welcome-cell/", width="100%", height="300px")
IMPORT ASSEMBLY
from biokbase.narrative.jobs.appmanager import AppManager
AppManager().run_app_bulk(
[{
"app_id": "kb_uploadmethods/import_fasta_as_assembly_from_staging",
"tag": "release",
"version": "31e93066beb421a51b9c8e44b1201aa93aea0b4e",
"params": [{
"staging_file_subdir_path": "assembly.fasta",
"assembly_name": "assembly.fasta",
"type": "draft isolate",
"min_contig_length": 500
}]
}],
cell_id="5ab9fd58-ad26-4dc1-ab16-9ab52fc9edb9",
run_id="b45244f5-ad49-435f-9e61-7da811ff7409"
)
ASSESS ASSEMBLY QUALITY
IMPORT RAW READS
from biokbase.narrative.jobs.appmanager import AppManager
AppManager().run_app_bulk(
[{
"app_id": "kb_uploadmethods/import_fastq_interleaved_as_reads_from_staging",
"tag": "release",
"version": "31e93066beb421a51b9c8e44b1201aa93aea0b4e",
"params": [{
"fastq_fwd_staging_file_name": "C9_S41_R2_001.fastq.gz",
"name": "C9_S41_R2_001.fastq.gz",
"sequencing_tech": "Illumina",
"single_genome": 1,
"read_orientation_outward": 0,
"insert_size_std_dev": None,
"insert_size_mean": None
}]
}],
cell_id="1d4117d0-6e2f-486c-b2ea-9a4b7db03235",
run_id="b61c5e83-9eee-46b8-b3ed-b91b328659e6"
)
from biokbase.narrative.jobs.appmanager import AppManager
AppManager().run_app_bulk(
[{
"app_id": "kb_uploadmethods/import_fastq_interleaved_as_reads_from_staging",
"tag": "release",
"version": "31e93066beb421a51b9c8e44b1201aa93aea0b4e",
"params": [{
"fastq_fwd_staging_file_name": "C9_S41_R1_001.fastq.gz",
"name": "C9_S41_R1_001.fastq.gz",
"sequencing_tech": "Illumina",
"single_genome": 1,
"read_orientation_outward": 0,
"insert_size_std_dev": None,
"insert_size_mean": None
}]
}],
cell_id="b48ff555-83b3-4292-a8f9-99b929319a8c",
run_id="2763ae14-59f3-4550-b841-c5da458bc78f"
)
| Created Object Name | Type | Description |
|---|---|---|
| C9_Trimmed_R1_R2_fastq.gz_paired | PairedEndLibrary | Trimmed Reads |
| C9_Trimmed_R1_R2_fastq.gz_unpaired_fwd | SingleEndLibrary | Trimmed Unpaired Forward Reads |
| C9_Trimmed_R1_R2_fastq.gz_unpaired_rev | SingleEndLibrary | Trimmed Unpaired Reverse Reads |
| Created Object Name | Type | Description |
|---|---|---|
| C9_R1_R2_hybridSPAdes.Assembly | Assembly | Assembled contigs |
MERGE READS
| C9_S41_R1_001.fastq.gz |
| C9_S41_R2_001.fastq.gz |
| Created Object Name | Type | Description |
|---|---|---|
| C9_R1_R2.readset | ReadsSet | KButil_Build_ReadsSet |
| C9_S41_R1_001.fastq.gz |
| C9_S41_R2_001.fastq.gz |
| Created Object Name | Type | Description |
|---|---|---|
| C9_S41_R1_R2.fastq.gz | PairedEndLibrary | R1 and R2 fastq of C9_Merge reads |
ASSESS READS QUALITY
CLASSIFY MICROBES
BIN CONTIGS
| C9_S41_R2_001.fastq.gz |
| C9_S41_R1_R2.fastq.gz |
| C9_S41_R1_001.fastq.gz |
| C9_S41_R2_001.fastq.gz |
| C9_S41_R1_R2.fastq.gz |
| Created Object Name | Type | Description |
|---|---|---|
| Bins.MaxBin2 | BinnedContigs | BinnedContigs from MaxBin2 |
| Bin.004.fasta |
| Created Object Name | Type | Description |
|---|---|---|
| Bin.004.fastaBin004_assembly | Assembly | Assembly object of extracted contigs |
| C9_R1_R2_hybridSPAdes.Assembly |
| Bin.004.fastaBin004_assembly |
| Bin.003.fastaBin003_assembly |
| Bin.003.fasta |
| Created Object Name | Type | Description |
|---|---|---|
| Bin.003.fastaBin003_assembly | Assembly | Assembly object of extracted contigs |
FILTER BINS BY QUALITY
| Created Object Name | Type | Description |
|---|---|---|
| CheckM_HQ_bins.BinnedContigs | BinnedContigs | HQ BinnedContigs CheckM_HQ_bins.BinnedContigs |
| Created Object Name | Type | Description |
|---|---|---|
| C9_R1_R2_CheckM_HQ_bins.BinnedContigs | BinnedContigs | HQ BinnedContigs C9_R1_R2_CheckM_HQ_bins.BinnedContigs |
| Created Object Name | Type | Description |
|---|---|---|
| CheckM_HQ_bins.MaxBin2.BinnedContigs | BinnedContigs | HQ BinnedContigs CheckM_HQ_bins.MaxBin2.BinnedContigs |
| Created Object Name | Type | Description |
|---|---|---|
| C9.HybridSpades.CheckM_HQ_bins.BinnedContigs | BinnedContigs | HQ BinnedContigs C9.HybridSpades.CheckM_HQ_bins.BinnedContigs |
ANNOTATE GENOME
| Created Object Name | Type | Description |
|---|---|---|
| Bin004.Prokka_annotate.genome | Genome | Annotated Genome |
| Bin.004.fastaBin004_assembly |
| Bin004.Prokka_annotate.genome |
| Created Object Name | Type | Description |
|---|---|---|
| Bin004Refs.pangenome | Pangenome | Pangenome |
| Created Object Name | Type | Description |
|---|---|---|
| Bin004Refs.genomecomparison | GenomeComparison | GenomeComparison |