M. tuberculosis Variant Analysis tutorial
Version 1

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Workflow Type: Galaxy

Galaxy workflow

SEEK ID: https://dev.workflowhub.eu/workflows/830?version=1

Inputs

ID Name Description Type
FASTA reference genome #main/FASTA reference genome n/a
  • File
Genbank reference genome #main/Genbank reference genome n/a
  • File
Genome annotation (GFF3) #main/Genome annotation (GFF3) n/a
  • File
Read 1 #main/Read 1 n/a
  • File
Read 2 #main/Read 2 n/a
  • File

Steps

ID Name Description
5 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0
6 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0
7 Trimmomatic toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1
8 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0
9 snippy toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/4.6.0+galaxy0
10 Kraken2 toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1
11 TB Variant Filter toolshed.g2.bx.psu.edu/repos/iuc/tb_variant_filter/tb_variant_filter/0.3.6+galaxy0
12 TB-Profiler Profile toolshed.g2.bx.psu.edu/repos/iuc/tbprofiler/tb_profiler_profile/4.4.1+galaxy0
13 JBrowse toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1
14 TB Variant Report toolshed.g2.bx.psu.edu/repos/iuc/tbvcfreport/tbvcfreport/0.1.10+galaxy0

Outputs

ID Name Description Type
mtbva_jbrowse #main/mtbva_jbrowse n/a
  • File
mtbva_kraken_report #main/mtbva_kraken_report n/a
  • File
mtbva_multiqc_webpage #main/mtbva_multiqc_webpage n/a
  • File
mtbva_snippy_variants_table #main/mtbva_snippy_variants_table n/a
  • File
mtbva_snippy_vcf #main/mtbva_snippy_vcf n/a
  • File
mtbva_tb_variant_dr_report_html #main/mtbva_tb_variant_dr_report_html n/a
  • File
mtbva_tb_variant_report_html #main/mtbva_tb_variant_report_html n/a
  • File

Version History

11 (earliest) Created 22nd Apr 2024 at 10:35 by Helena Rasche

Added/updated 3 files


Open master 65a4318
help Creators and Submitter
Creator
  • Peter van Heusden
Submitter
Tools
FastQC
Trimmomatic
MultiQC
snippy
kraken2
COMBAT-TB Workbench
tb-profiler
JBrowse
License
MIT License
Activity

Views: 48

Created: 22nd Apr 2024 at 10:35

Last updated: 22nd Apr 2024 at 10:35

help Attributions

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Total size: 40.3 KB
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