Quality and contamination control in bacterial isolate using Illumina MiSeq Data
1.0

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Workflow Type: Galaxy

Quality and contamination control in bacterial isolate using Illumina MiSeq Data

Associated Tutorial

This workflows is part of the tutorial Quality and contamination control in bacterial isolate using Illumina MiSeq Data, available in the GTN

Features

Thanks to...

Tutorial Author(s): Bérénice Batut, Clea Siguret

Workflow Author(s): Bérénice Batut, Clea Siguret

Funder(s): ABRomics

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1344?version=1

Inputs

ID Name Description Type
DRR187559_1 #main/DRR187559_1 forward read
  • File
DRR187559_2 #main/DRR187559_2 reverse read
  • File

Steps

ID Name Description
2 FastQC (forward) toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0
3 FastQC (reverse) toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0
4 fastp toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0
5 Kraken2 toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1
6 Bracken toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/2.8+galaxy0
7 Recentrifuge toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.12.1+galaxy0

Outputs

ID Name Description Type
DRR187559_filtered_ #main/DRR187559_filtered_ n/a
  • File
DRR187559_filtered_1 #main/DRR187559_filtered_1 n/a
  • File
FastQC html_file (forward) #main/FastQC html_file (forward) n/a
  • File
FastQC html_file (reverse) #main/FastQC html_file (reverse) n/a
  • File
FastQC text_file (forward) #main/FastQC text_file (forward) n/a
  • File
FastQC text_file (reverse) #main/FastQC text_file (reverse) n/a
  • File
bracken_kraken_report #main/bracken_kraken_report n/a
  • File
bracken_report_tsv #main/bracken_report_tsv n/a
  • File
fastp report_html #main/fastp report_html n/a
  • File
fastp_json #main/fastp_json n/a
  • File
kraken_report_reads #main/kraken_report_reads n/a
  • File
kraken_report_tabular #main/kraken_report_tabular n/a
  • File
recentrifuge_data_tabular #main/recentrifuge_data_tabular n/a
  • File
recentrifuge_logfile #main/recentrifuge_logfile n/a
  • File
recentrifuge_report_html #main/recentrifuge_report_html n/a
  • File
recentrifuge_stats_tabular #main/recentrifuge_stats_tabular n/a
  • File

Version History

1.0 (earliest) Created 15th Jul 2024 at 14:09 by Helena Rasche

Added/updated 4 files


Open master 36d87db
help Creators and Submitter
Creators
Not specified
Submitter
Discussion Channel
GTN Matrix
Tools
FastQC
fastp
kraken2
Bracken
Recentrifuge
License
GNU General Public License v3.0 or later
Activity

Views: 229   Downloads: 63

Created: 15th Jul 2024 at 14:09

Last updated: 15th Jul 2024 at 14:09

help Attributions

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Total size: 128 KB
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