TB Variant Analysis v1.0
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Run on GalaxyPredict variants and drug resistance from M. tuberculosis sequence samples (Illumina)
Associated Tutorial
This workflows is part of the tutorial M. tuberculosis Variant Analysis, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a Galaxy Workflow Report
Thanks to...
Workflow Author(s): Peter van Heusden, Tristan Reynolds
Tutorial Author(s): Peter van Heusden, Simon Gladman, Thoba Lose
Tutorial Contributor(s): Tristan Reynolds, Helena Rasche, Linelle Abueg, Wolfgang Maier, Saskia Hiltemann, Cristóbal Gallardo, Björn Grüning, Bérénice Batut, Peter van Heusden, Anthony Bretaudeau, Mélanie Petera
Funder(s): The University of Melbourne, Melbourne Bioinformatics, Australian BioCommons
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 |
|
| Minimum depth of coverage | Minimum depth of coverage | Minimum depth of coverage for a position on the genome |
|
| Minimum variant allele frequency | Minimum variant allele frequency | Minimum proportion of reads that must support a variant for it to be called |
|
| Reads | Reads | List of paired Illumina reads (set format to fastqsanger or fastqsanger.gz as appropriate) |
|
| Reference Genome | Reference Genome | M. tuberculosis reference genome (must be in H37Rv coordinates. The M. tuberculosis inferred ancestral genome is recommended) |
|
Steps
| ID | Name | Description |
|---|---|---|
| 5 | fastp | toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/1.0.1+galaxy3 |
| 6 | seqret | toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: seqret84/5.0.0 |
| 7 | Kraken2 | toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.17.1+galaxy0 |
| 8 | snippy | toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/4.6.0+galaxy0 |
| 9 | TB Variant Filter | toolshed.g2.bx.psu.edu/repos/iuc/tb_variant_filter/tb_variant_filter/0.4.0+galaxy0 |
| 10 | TB Variant Filter | toolshed.g2.bx.psu.edu/repos/iuc/tb_variant_filter/tb_variant_filter/0.4.0+galaxy0 |
| 11 | QualiMap BamQC | toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.3+galaxy0 |
| 12 | TB-Profiler Profile | toolshed.g2.bx.psu.edu/repos/iuc/tbprofiler/tb_profiler_profile/6.6.4+galaxy0 |
| 13 | mosdepth | toolshed.g2.bx.psu.edu/repos/iuc/mosdepth/mosdepth/0.3.12+galaxy0 |
| 14 | Text transformation | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.5+galaxy2 |
| 15 | Flatten collection | __FLATTEN__ |
| 16 | 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/9.5+galaxy2 |
| 17 | TB Variant Report | toolshed.g2.bx.psu.edu/repos/iuc/tbvcfreport/tbvcfreport/1.0.1+galaxy0 |
| 18 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy4 |
| 19 | 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+galaxy4 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| output | output | n/a |
|
| report_output | report_output | n/a |
|
| output_txt | output_txt | n/a |
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| Final annotated VCF | Final annotated VCF | n/a |
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| variants_report_html | variants_report_html | n/a |
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| drug_resistance_report_html | drug_resistance_report_html | n/a |
|
| html_report | html_report | n/a |
|
| consensus_genome | consensus_genome | n/a |
|
Version History
master
7.0
Creators and Submitter
Views: 2491 Downloads: 364 Runs: 2
Created: 2nd Jun 2025 at 11:02
Last updated: 12th Jan 2026 at 13:17
Tags AttributionsNone
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