TB Variant Analysis v1.0

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Workflow Type: Galaxy

Predict variants and drug resistance from M. tuberculosis sequence samples (Illumina)

Associated Tutorial

This workflows is part of the tutorial TB Variant Analysis v1.0, available in the GTN

Features

Thanks to...

Tutorial Author(s): Peter van Heusden, Simon Gladman, Thoba Lose

Workflow Author(s): Peter van Heusden

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1069?version=1

Inputs

ID Name Description Type
Additional BWA-MEM options Additional BWA-MEM options Increasing the minimum seed length (-k) parameter can help eliminate matches from contaminants. If used this should be set to 2/3rds of the read length, i.e. the string "-k 100" should be used for 150 base pair reads
  • string?
Minimum depth of coverage Minimum depth of coverage Minimum depth of coverage for a position on the genome
  • int?
Minimum variant allele frequency Minimum variant allele frequency Minimum proportion of reads that must support a variant for it to be called
  • float?
Reads Reads List of paired Illumina reads (set format to fastqsanger or fastqsanger.gz as appropriate)
  • File[]
Reference Genome Reference Genome M. tuberculosis reference genome (must be in H37Rv coordinates. The M. tuberculosis inferred ancestral genome is recommended)
  • File

Steps

ID Name Description
5 fastp toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0
6 seqret toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: seqret84/5.0.0
7 snippy toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/4.6.0+galaxy0
8 Kraken2 toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1
9 QualiMap BamQC toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2c+galaxy1
10 mosdepth toolshed.g2.bx.psu.edu/repos/iuc/mosdepth/mosdepth/0.3.8+galaxy0
11 TB Variant Filter toolshed.g2.bx.psu.edu/repos/iuc/tb_variant_filter/tb_variant_filter/0.4.0+galaxy0
12 TB-Profiler Profile toolshed.g2.bx.psu.edu/repos/iuc/tbprofiler/tb_profiler_profile/6.2.1+galaxy0
13 TB Variant Filter toolshed.g2.bx.psu.edu/repos/iuc/tb_variant_filter/tb_variant_filter/0.4.0+galaxy0
14 Flatten collection __FLATTEN__
15 Text reformatting bcftools consensus requires a region file of low coverage regions in 1 based coordinates, mosdepth produces one in BED format with LOW and PASS for low coverage and non-low coverage regions. This converts from the one format to the other. toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1
16 Text transformation toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1
17 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1
18 bcftools consensus Compute consensus genome with single nucleotide variants inserted, suitable for use in building a phylogeny toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy3
19 TB Variant Report toolshed.g2.bx.psu.edu/repos/iuc/tbvcfreport/tbvcfreport/1.0.0+galaxy0

Outputs

ID Name Description Type
report_output report_output n/a
  • File
output output n/a
  • File
output_txt output_txt n/a
  • File
Final annotated VCF Final annotated VCF n/a
  • File
html_report html_report n/a
  • File
consensus_genome consensus_genome n/a
  • File
drug_resistance_report_html drug_resistance_report_html n/a
  • File
variants_report_html variants_report_html n/a
  • File

Version History

7.0 (latest) Created 16th Jul 2024 at 14:09 by Helena Rasche

Added/updated 4 files


Open master d6f4ed5

14.0 (earliest) Created 25th Jun 2024 at 10:54 by Helena Rasche

Added/updated 4 files


Frozen 14.0 384a6af
help Creators and Submitter
Creators
Not specified
Submitter
Discussion Channel
GTN Matrix
Tools
fastp
snippy
kraken2
QualiMap
COMBAT-TB Workbench
tb-profiler
MultiQC
BCFtools
License
GNU Affero General Public License v3.0 or later
Activity

Views: 567   Downloads: 161

Created: 25th Jun 2024 at 10:54

Last updated: 25th Jun 2024 at 10:54

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Total size: 198 KB
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