TB Variant Analysis v1.0
Version 1

Workflow Type: Galaxy
Stable

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

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
output output n/a
  • File
report_output report_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

Version 1 (earliest) Created 7th Jun 2024 at 20:07 by Peter van Heusden

Initial commit


Open master f9ec668
help Creators and Submitter
Creator
  • Peter van Heusden
Submitter
Activity

Views: 128   Downloads: 10

Created: 7th Jun 2024 at 20:07

Last updated: 12th Jun 2024 at 14:38

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