Generated August 14, 2020

Taxonomic analysis of avocado (Persea americana) bark and rhizosphere soil samples

Data analysis for the article:

Bark from Avocado Trees of Different Geographic Locations have Consistent Microbial Communities

Eneas Aguirre-von-Wobeser1*, Alexandro Alonso-Sánchez2, Alfonso Méndez-Bravo3, Luis Alberto Villanueva Espino3, Frédérique Reverchon2

1CONACYT – Centro de Investigación y Desarrollo en Agrobiotecnología Alimentaria, Centro de Investigación y Desarrollo, A.C., Blvd. Sta. Catarina s/n, Col. Santiago Tlapacoya, 42110, San Agustín Tlaxiaca, Hidalgo, Mexico

2Red de Estudios Moleculares Avanzados, Instituto de Ecología, A.C. Carretera antigua a Coatepec 351, Col. El Haya, 91070, Xalapa, Veracruz, Mexico

3CONACYT – Escuela Nacional de Estudios Superiores, Laboratorio Nacional de Análisis y Síntesis Ecológica, Universidad Nacional Autónoma de México, Antigua Carretera a Pátzcuaro 8701, Col. Ex-Hacienda de San José de La Huerta, 58190, Morelia, Michoacán, Mexico

*Correspondance: E. Aguirre-von-Wobeser eneas.aguirre@ciad.mx

Instuctions to view complete taxonomic composition of avocado bark and rhizospheric soil samples:

  1. Go to the section Kaiju taxonomic analysis interactive plots.
  2. Scroll down to the desired sample.
  3. Click on "View Report in Separate Window"
  4. Click the link on the upper right, ending with the word "Krona"
  5. In the plot, click on the different taxonomic groups to zoom in and out.

Contents

  1. Sampling procedure
  2. DNA extraction and library preparation
  3. Sequencing
  4. Sample description
  5. Raw reads data objects
  6. Funding
  7. Import data
  8. Cleaning reads
  9. Merge reads
  10. Kaiju taxonomic analysis interactive plots

1. Sampling procedure

Please refer to the manuscript for details on the methods and sampling sites.

Bark samples were collected using a sterile knife (aprox. 5 x 5 slices).

Rhizosphere samples were collected with a sterile spoon at Persea americana roots.

Samples were frozen and transported to the laboratory, where they were stored at -80°C.

2. DNA extraction and library preparation

DNA was extracted using a DNeasy PowerSoil kit (QIAGEN). Bark samples were cut in small pieces and inserted directly into the kits vials

Libraries were prepared with a Nextera DNA Flex kit

3. Sequencing

Seqeuencing was performed on a NextSeq 550 instrument with a 2 x 150 kit.

4. Sample description

  • A1. Avocado Bark from Malinalco.
  • A1. Avocado Bark from Malinalco.
  • A1. Avocado Bark from Malinalco.
  • SA1. Avocado Rhizospheric Soil from Malinalco.
  • SA2. Avocado Rhizospheric Soil from Malinalco.
  • SA4. Avocado Rhizospheric Soil from Malinalco.
  • SA5. Avocado Rhizospheric Soil from Malinalco.
  • A1. Avocado Bark from Morelia.
  • A1. Avocado Bark from Morelia.

5. Raw data

Instructions to download raw data

  1. Sin into KBase at www.kbase.us
  2. Go to the KBase narrative at https://narrative.kbase.us/narrative/69195
  3. Select the data of interest from the table below.
  4. At the data panel at the left, hover on the sample object, and click on "..." to open.
  5. Click the download icon to start download.
Object Description
EAVMMArA01_S10_L001_R1_001.fastq.gz_reads Sample A1 Lane 1, raw reads
EAVMMArA01_S10_L002_R1_001.fastq.gz_reads Sample A1 Lane 2, raw reads
EAVMMArA01_S10_L003_R1_001.fastq.gz_reads Sample A1 Lane 3, raw reads
EAVMMArA01_S10_L004_R1_001.fastq.gz_reads Sample A1 Lane 4, raw reads
EAVMMArA03_S4_L001_R1_001.fastq.gz_reads Sample A4 Lane 1, raw reads
EAVMMArA03_S4_L002_R1_001.fastq.gz_reads Sample A4 Lane 2, raw reads
EAVMMArA03_S4_L003_R1_001.fastq.gz_reads Sample A4 Lane 3, raw reads
EAVMMArA03_S4_L004_R1_001.fastq.gz_reads Sample A4 Lane 4, raw reads
EAVMMArA04_S3_L001_R1_001.fastq.gz_reads Sample A5 Lane 1, raw reads
EAVMMArA04_S3_L002_R1_001.fastq.gz_reads Sample A5 Lane 2, raw reads
EAVMMArA04_S3_L003_R1_001.fastq.gz_reads Sample A5 Lane 3, raw reads
EAVMMArA04_S3_L004_R1_001.fastq.gz_reads Sample A5 Lane 4, raw reads
EAVMMArA05_S5_L001_R1_001.fastq.gz_reads Sample SA1 Lane 1, raw reads
EAVMMArA05_S5_L002_R1_001.fastq.gz_reads Sample SA1 Lane 2, raw reads
EAVMMArA05_S5_L003_R1_001.fastq.gz_reads Sample SA1 Lane 3, raw reads
EAVMMArA05_S5_L004_R1_001.fastq.gz_reads Sample SA1 Lane 4, raw reads
EAVMMArA06_S11_L001_R1_001.fastq.gz_reads Sample SA2 Lane 1, raw reads
EAVMMArA06_S11_L002_R1_001.fastq.gz_reads Sample SA2 Lane 2, raw reads
EAVMMArA06_S11_L003_R1_001.fastq.gz_reads Sample SA2 Lane 3, raw reads
EAVMMArA06_S11_L004_R1_001.fastq.gz_reads Sample SA2 Lane 4, raw reads
EAVMMArA07_S9_L001_R1_001.fastq.gz_reads Sample SA4 Lane 1, raw reads
EAVMMArA07_S9_L002_R1_001.fastq.gz_reads Sample SA4 Lane 2, raw reads
EAVMMArA07_S9_L003_R1_001.fastq.gz_reads Sample SA4 Lane 3, raw reads
EAVMMArA07_S9_L004_R1_001.fastq.gz_reads Sample SA4 Lane 4, raw reads
EAVMMArA08_S2_L001_R1_001.fastq.gz_reads Sample SA5 Lane 1, raw reads
EAVMMArA08_S2_L002_R1_001.fastq.gz_reads Sample SA5 Lane 2, raw reads
EAVMMArA08_S2_L003_R1_001.fastq.gz_reads Sample SA5 Lane 3, raw reads
EAVMMArA08_S2_L004_R1_001.fastq.gz_reads Sample SA5 Lane 4, raw reads
EAVMMArA11_S6_L001_R1_001.fastq.gz_reads Sample M5 Lane 1, raw reads
EAVMMArA11_S6_L002_R1_001.fastq.gz_reads Sample M5 Lane 2, raw reads
EAVMMArA11_S6_L003_R1_001.fastq.gz_reads Sample M5 Lane 3, raw reads
EAVMMArA11_S6_L004_R1_001.fastq.gz_reads Sample M5 Lane 4, raw reads
EAVMMArA12_S1_L001_R1_001.fastq.gz_reads Sample M6 Lane 1, raw reads
EAVMMArA12_S1_L002_R1_001.fastq.gz_reads Sample M6 Lane 2, raw reads
EAVMMArA12_S1_L003_R1_001.fastq.gz_reads Sample M6 Lane 3, raw reads
EAVMMArA12_S1_L004_R1_001.fastq.gz_reads Sample M6 Lane 4, raw reads

6. Funding

SEP/CONACyT grant number CB-2014-01-242956

v1 - KBaseFile.PairedEndLibrary-2.1
The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/69195

Import reads from Sample A1

Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 11m 38s.
Objects
Created Object Name Type Description
EAVMMArA01_S10_L001_R1_001.fastq.gz_reads PairedEndLibrary Imported Reads
Links
Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 12m 1s.
Objects
Created Object Name Type Description
EAVMMArA01_S10_L002_R1_001.fastq.gz_reads PairedEndLibrary Imported Reads
Links
Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 11m 46s.
Objects
Created Object Name Type Description
EAVMMArA01_S10_L003_R1_001.fastq.gz_reads PairedEndLibrary Imported Reads
Links
Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 11m 45s.
Objects
Created Object Name Type Description
EAVMMArA01_S10_L004_R1_001.fastq.gz_reads PairedEndLibrary Imported Reads
Links

Import reads from sample A4

Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 16m 46s.
Objects
Created Object Name Type Description
EAVMMArA03_S4_L001_R1_001.fastq.gz_reads PairedEndLibrary Imported Reads
Links
Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 17m 9s.
Objects
Created Object Name Type Description
EAVMMArA03_S4_L002_R1_001.fastq.gz_reads PairedEndLibrary Imported Reads
Links
Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 16m 46s.
Objects
Created Object Name Type Description
EAVMMArA03_S4_L003_R1_001.fastq.gz_reads PairedEndLibrary Imported Reads
Links
Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 16m 44s.
Objects
Created Object Name Type Description
EAVMMArA03_S4_L004_R1_001.fastq.gz_reads PairedEndLibrary Imported Reads
Links

Import reads from sample A5

Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 26m 43s.
Objects
Created Object Name Type Description
EAVMMArA04_S3_L001_R1_001.fastq.gz_reads PairedEndLibrary Imported Reads
Links
Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 26m 38s.
Objects
Created Object Name Type Description
EAVMMArA04_S3_L002_R1_001.fastq.gz_reads PairedEndLibrary Imported Reads
Links
Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 31m 44s.
Objects
Created Object Name Type Description
EAVMMArA04_S3_L003_R1_001.fastq.gz_reads PairedEndLibrary Imported Reads
Links
Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 26m 41s.
Objects
Created Object Name Type Description
EAVMMArA04_S3_L004_R1_001.fastq.gz_reads PairedEndLibrary Imported Reads
Links

Import reads from sample SA1

Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 11m 60s.
Objects
Created Object Name Type Description
EAVMMArA05_S5_L001_R1_001.fastq.gz_reads PairedEndLibrary Imported Reads
Links
Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 12m 1s.
Objects
Created Object Name Type Description
EAVMMArA05_S5_L002_R1_001.fastq.gz_reads PairedEndLibrary Imported Reads
Links
Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 11m 49s.
Objects
Created Object Name Type Description
EAVMMArA05_S5_L003_R1_001.fastq.gz_reads PairedEndLibrary Imported Reads
Links
Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 11m 45s.
Objects
Created Object Name Type Description
EAVMMArA05_S5_L004_R1_001.fastq.gz_reads PairedEndLibrary Imported Reads
Links

Import reads from sample SA2

Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 11m 43s.
Objects
Created Object Name Type Description
EAVMMArA06_S11_L001_R1_001.fastq.gz_reads PairedEndLibrary Imported Reads
Links
Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 11m 41s.
Objects
Created Object Name Type Description
EAVMMArA06_S11_L002_R1_001.fastq.gz_reads PairedEndLibrary Imported Reads
Links
Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 11m 42s.
Objects
Created Object Name Type Description
EAVMMArA06_S11_L003_R1_001.fastq.gz_reads PairedEndLibrary Imported Reads
Links
Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 11m 41s.
Objects
Created Object Name Type Description
EAVMMArA06_S11_L004_R1_001.fastq.gz_reads PairedEndLibrary Imported Reads
Links

Import reads from smple SA4

Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 11m 34s.
Objects
Created Object Name Type Description
EAVMMArA07_S9_L001_R1_001.fastq.gz_reads PairedEndLibrary Imported Reads
Links
Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 11m 41s.
Objects
Created Object Name Type Description
EAVMMArA07_S9_L003_R1_001.fastq.gz_reads PairedEndLibrary Imported Reads
Links
Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 11m 42s.
Objects
Created Object Name Type Description
EAVMMArA07_S9_L004_R1_001.fastq.gz_reads PairedEndLibrary Imported Reads
Links
Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 11m 44s.
Objects
Created Object Name Type Description
EAVMMArA07_S9_L002_R1_001.fastq.gz_reads PairedEndLibrary Imported Reads
Links

Import reads from ample SA5

Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 11m 38s.
Objects
Created Object Name Type Description
EAVMMArA08_S2_L001_R1_001.fastq.gz_reads PairedEndLibrary Imported Reads
Links
Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 11m 42s.
Objects
Created Object Name Type Description
EAVMMArA08_S2_L002_R1_001.fastq.gz_reads PairedEndLibrary Imported Reads
Links
Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 11m 45s.
Objects
Created Object Name Type Description
EAVMMArA08_S2_L003_R1_001.fastq.gz_reads PairedEndLibrary Imported Reads
Links
Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 11m 44s.
Objects
Created Object Name Type Description
EAVMMArA08_S2_L004_R1_001.fastq.gz_reads PairedEndLibrary Imported Reads
Links

Import reads from sample M5

Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 16m 33s.
Objects
Created Object Name Type Description
EAVMMArA11_S6_L003_R1_001.fastq.gz_reads PairedEndLibrary Imported Reads
Links
Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 16m 36s.
Objects
Created Object Name Type Description
EAVMMArA11_S6_L004_R1_001.fastq.gz_reads PairedEndLibrary Imported Reads
Links
Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 5h 28m 18s.
Objects
Created Object Name Type Description
EAVMMArA11_S6_L002_R1_001.fastq.gz_reads PairedEndLibrary Imported Reads
Links
Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 8h 44m 22s.
Objects
Created Object Name Type Description
EAVMMArA11_S6_L001_R1_001.fastq.gz_reads PairedEndLibrary Imported Reads
Links

Import reads from ample M6

Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 22m 49s.
Objects
Created Object Name Type Description
EAVMMArA12_S1_L003_R1_001.fastq.gz_reads PairedEndLibrary Imported Reads
Links
Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 3h 48m 48s.
Objects
Created Object Name Type Description
EAVMMArA12_S1_L002_R1_001.fastq.gz_reads PairedEndLibrary Imported Reads
Links
Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 17m 11s.
Objects
Created Object Name Type Description
EAVMMArA12_S1_L004_R1_001.fastq.gz_reads PairedEndLibrary Imported Reads
Links
Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 2h 49m 12s.
Objects
Created Object Name Type Description
EAVMMArA12_S1_L001_R1_001.fastq.gz_reads PairedEndLibrary Imported Reads
Links

Trim reads sample A1.

Bark from Malinalco

Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 1h 5m 20s.
Objects
Created Object Name Type Description
A01_S10_L004_R1_001.fastq.gz_reads_trimmed_paired PairedEndLibrary Trimmed Reads
A01_S10_L004_R1_001.fastq.gz_reads_trimmed_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
A01_S10_L004_R1_001.fastq.gz_reads_trimmed_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 25m 0s.
Objects
Created Object Name Type Description
A01_S10_L002_R1_001.fastq.gz_rads.trimmed_paired PairedEndLibrary Trimmed Reads
A01_S10_L002_R1_001.fastq.gz_rads.trimmed_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
A01_S10_L002_R1_001.fastq.gz_rads.trimmed_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 21m 18s.
Objects
Created Object Name Type Description
A01_S1_L001_R1_001.fastq_paired PairedEndLibrary Trimmed Reads
A01_S1_L001_R1_001.fastq_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
A01_S1_L001_R1_001.fastq_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 16m 37s.
Objects
Created Object Name Type Description
A01_S10_L003_R1_001.fastq.gz_reads_trimmed_paired PairedEndLibrary Trimmed Reads
A01_S10_L003_R1_001.fastq.gz_reads_trimmed_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
A01_S10_L003_R1_001.fastq.gz_reads_trimmed_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads

Trim reads sample A4.

Bark from Malinalco

Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 37m 35s.
Objects
Created Object Name Type Description
A03_S4_L001_R1_001.fastq.gz_reads_trimmed_paired PairedEndLibrary Trimmed Reads
A03_S4_L001_R1_001.fastq.gz_reads_trimmed_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
A03_S4_L001_R1_001.fastq.gz_reads_trimmed_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 36m 59s.
Objects
Created Object Name Type Description
A03_S4_L002_R1_001.fastq.gz_reads_trimmed_paired PairedEndLibrary Trimmed Reads
A03_S4_L002_R1_001.fastq.gz_reads_trimmed_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
A03_S4_L002_R1_001.fastq.gz_reads_trimmed_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 25m 26s.
Objects
Created Object Name Type Description
A03_S4_L004_R1_001.fastq.gz_reads_paired PairedEndLibrary Trimmed Reads
A03_S4_L004_R1_001.fastq.gz_reads_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
A03_S4_L004_R1_001.fastq.gz_reads_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 25m 13s.
Objects
Created Object Name Type Description
A03_S4_L003_R1_001.fastq.gz_reads_trimmed_paired PairedEndLibrary Trimmed Reads
A03_S4_L003_R1_001.fastq.gz_reads_trimmed_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
A03_S4_L003_R1_001.fastq.gz_reads_trimmed_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads

Trim reads from sample A5

Bark from Malinalco.

Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 1h 20m 11s.
Objects
Created Object Name Type Description
A04_S3_L001_R1_001.fastq.gz_reads_trimmed_paired PairedEndLibrary Trimmed Reads
A04_S3_L001_R1_001.fastq.gz_reads_trimmed_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
A04_S3_L001_R1_001.fastq.gz_reads_trimmed_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 55m 51s.
Objects
Created Object Name Type Description
A04_S3_L002_R1_001.fastq.gz_reads_trimmed_paired PairedEndLibrary Trimmed Reads
A04_S3_L002_R1_001.fastq.gz_reads_trimmed_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
A04_S3_L002_R1_001.fastq.gz_reads_trimmed_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 1h 49m 59s.
Objects
Created Object Name Type Description
A04_S3_L003_R1_001.fastq.gz_reads_trimmed_paired PairedEndLibrary Trimmed Reads
A04_S3_L003_R1_001.fastq.gz_reads_trimmed_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
A04_S3_L003_R1_001.fastq.gz_reads_trimmed_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 58m 28s.
Objects
Created Object Name Type Description
A04_S3_L004_R1_001.fastq.gz_reads_trimmed_paired PairedEndLibrary Trimmed Reads
A04_S3_L004_R1_001.fastq.gz_reads_trimmed_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
A04_S3_L004_R1_001.fastq.gz_reads_trimmed_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads

Trim reads from sample SA1

Rhizospheric soil from Malinalco

Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 16m 10s.
Objects
Created Object Name Type Description
A05_S5_L001_R1_001.fastq.gz_reads_trimmed_paired PairedEndLibrary Trimmed Reads
A05_S5_L001_R1_001.fastq.gz_reads_trimmed_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
A05_S5_L001_R1_001.fastq.gz_reads_trimmed_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 14m 46s.
Objects
Created Object Name Type Description
A05_S5_L002_R1_001.fastq.gz_reads_trimmed_paired PairedEndLibrary Trimmed Reads
A05_S5_L002_R1_001.fastq.gz_reads_trimmed_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
A05_S5_L002_R1_001.fastq.gz_reads_trimmed_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 20m 45s.
Objects
Created Object Name Type Description
A05_S5_L003_R1_001.fastq.gz_reads_trimmed_paired PairedEndLibrary Trimmed Reads
A05_S5_L003_R1_001.fastq.gz_reads_trimmed_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
A05_S5_L003_R1_001.fastq.gz_reads_trimmed_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 22m 8s.
Objects
Created Object Name Type Description
A05_S5_L004_R1_001.fastq.gz.reads_trimmed_paired PairedEndLibrary Trimmed Reads
A05_S5_L004_R1_001.fastq.gz.reads_trimmed_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
A05_S5_L004_R1_001.fastq.gz.reads_trimmed_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads

Trim reads from sample SA2

Rhisospheric soil from Malinalco.

Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 38m 32s.
Objects
Created Object Name Type Description
A06_S11_L001_R1_001.fastq.gz_reads_paired PairedEndLibrary Trimmed Reads
A06_S11_L001_R1_001.fastq.gz_reads_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
A06_S11_L001_R1_001.fastq.gz_reads_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 37m 49s.
Objects
Created Object Name Type Description
A06_S11_L003_R1_001.fastq.gz_reads_trimmed_paired PairedEndLibrary Trimmed Reads
A06_S11_L003_R1_001.fastq.gz_reads_trimmed_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
A06_S11_L003_R1_001.fastq.gz_reads_trimmed_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 1h 3m 39s.
Objects
Created Object Name Type Description
A06_S11_L004_R1_001.fastq.gz_reads_trimmed_paired PairedEndLibrary Trimmed Reads
A06_S11_L004_R1_001.fastq.gz_reads_trimmed_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
A06_S11_L004_R1_001.fastq.gz_reads_trimmed_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 37m 2s.
Objects
Created Object Name Type Description
A06_S11_L002_R1_001.fastq.gz_reads_trimmed_paired PairedEndLibrary Trimmed Reads
A06_S11_L002_R1_001.fastq.gz_reads_trimmed_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
A06_S11_L002_R1_001.fastq.gz_reads_trimmed_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads

Trim reads from sample SA4

Rhizospheric soil from Malinalco.

Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 37m 4s.
Objects
Created Object Name Type Description
A07_S9_L001_R1_001.fastq.qz_reads_trimmed_paired PairedEndLibrary Trimmed Reads
A07_S9_L001_R1_001.fastq.qz_reads_trimmed_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
A07_S9_L001_R1_001.fastq.qz_reads_trimmed_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 42m 29s.
Objects
Created Object Name Type Description
A07_S9_L002_R1_001.fastq.gz_reads_trimmed_paired PairedEndLibrary Trimmed Reads
A07_S9_L002_R1_001.fastq.gz_reads_trimmed_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
A07_S9_L002_R1_001.fastq.gz_reads_trimmed_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 1h 7m 42s.
Objects
Created Object Name Type Description
A07_S9_L003_R1_001.fastq.gz_reads_trimmed_paired PairedEndLibrary Trimmed Reads
A07_S9_L003_R1_001.fastq.gz_reads_trimmed_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
A07_S9_L003_R1_001.fastq.gz_reads_trimmed_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 41m 31s.
Objects
Created Object Name Type Description
A07_S9_L004_R1_001.fastq.gz_reads_trimmed_paired PairedEndLibrary Trimmed Reads
A07_S9_L004_R1_001.fastq.gz_reads_trimmed_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
A07_S9_L004_R1_001.fastq.gz_reads_trimmed_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads

Trim reads from sample SA5

Rhizospheric soil from Malinalco.

Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 1h 11m 50s.
Objects
Created Object Name Type Description
A08_S2_L001_R1_001.fastq.gz_reads_trimmed_paired PairedEndLibrary Trimmed Reads
A08_S2_L001_R1_001.fastq.gz_reads_trimmed_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
A08_S2_L001_R1_001.fastq.gz_reads_trimmed_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 36m 58s.
Objects
Created Object Name Type Description
A08_S2_L002_R1_001.fastq.gz_reads_trimmed_paired PairedEndLibrary Trimmed Reads
A08_S2_L002_R1_001.fastq.gz_reads_trimmed_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
A08_S2_L002_R1_001.fastq.gz_reads_trimmed_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 1h 18m 43s.
Objects
Created Object Name Type Description
A08_S2_L003_R1_002.fastq.gz_reads_trimmed_paired PairedEndLibrary Trimmed Reads
A08_S2_L003_R1_002.fastq.gz_reads_trimmed_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
A08_S2_L003_R1_002.fastq.gz_reads_trimmed_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 36m 20s.
Objects
Created Object Name Type Description
A08_S2_L004_R1_001.fastq.gz_reads_trimmed_paired PairedEndLibrary Trimmed Reads
A08_S2_L004_R1_001.fastq.gz_reads_trimmed_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
A08_S2_L004_R1_001.fastq.gz_reads_trimmed_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads

Trim reads from sample M5

Rhizospheric soil from Morelia.

Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 45m 2s.
Objects
Created Object Name Type Description
A11_S6_L002_R1_001.fastq.gz_reads_trimmed_paired PairedEndLibrary Trimmed Reads
A11_S6_L002_R1_001.fastq.gz_reads_trimmed_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
A11_S6_L002_R1_001.fastq.gz_reads_trimmed_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 52m 13s.
Objects
Created Object Name Type Description
A11_S6_L001_R1_001.fastq.gz_reads_trimmed_paired PairedEndLibrary Trimmed Reads
A11_S6_L001_R1_001.fastq.gz_reads_trimmed_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
A11_S6_L001_R1_001.fastq.gz_reads_trimmed_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 56m 22s.
Objects
Created Object Name Type Description
A11_S6_L003_R1_001.fastq.gz_reads_trimmed_paired PairedEndLibrary Trimmed Reads
A11_S6_L003_R1_001.fastq.gz_reads_trimmed_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
A11_S6_L003_R1_001.fastq.gz_reads_trimmed_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 55m 45s.
Objects
Created Object Name Type Description
A11_S6_L004_R1_001-fastq.gz_reads_trimmed_paired PairedEndLibrary Trimmed Reads
A11_S6_L004_R1_001-fastq.gz_reads_trimmed_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
A11_S6_L004_R1_001-fastq.gz_reads_trimmed_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads

Trim reads from sample M6

Bark from Morelia.

Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 29m 59s.
Objects
Created Object Name Type Description
A12_S1_L003_R1_001.fastq.qz_reads_trimmed_paired PairedEndLibrary Trimmed Reads
A12_S1_L003_R1_001.fastq.qz_reads_trimmed_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
A12_S1_L003_R1_001.fastq.qz_reads_trimmed_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 36m 22s.
Objects
Created Object Name Type Description
A12_S1_L001_R1_001.fastq.gz_reads_trimmed_paired PairedEndLibrary Trimmed Reads
A12_S1_L001_R1_001.fastq.gz_reads_trimmed_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
A12_S1_L001_R1_001.fastq.gz_reads_trimmed_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 32m 32s.
Objects
Created Object Name Type Description
A12_S1_L002_R1_001.fastq.gz.reads_trimmed_paired PairedEndLibrary Trimmed Reads
A12_S1_L002_R1_001.fastq.gz.reads_trimmed_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
A12_S1_L002_R1_001.fastq.gz.reads_trimmed_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 24m 14s.
Objects
Created Object Name Type Description
A12_S1_L004_R1_001.fastq.gz_reads_trimmed_paired PairedEndLibrary Trimmed Reads
A12_S1_L004_R1_001.fastq.gz_reads_trimmed_unpaired_fwd SingleEndLibrary Trimmed Unpaired Forward Reads
A12_S1_L004_R1_001.fastq.gz_reads_trimmed_unpaired_rev SingleEndLibrary Trimmed Unpaired Reverse Reads

Merge all reads from sample A1

Bark from Malinalco.

Merge multiple Reads Libraries and/or ReadsSets into one Reads Library object.
This app completed without errors in 1h 22m 22s