From Fastqs to VCFs and BAMs
1.0

Workflow Type: Galaxy

From Fastqs to VCFs and BAMs

Associated Tutorial

This workflows is part of the tutorial Identifying tuberculosis transmission links: from SNPs to transmission clusters, available in the GTN

Thanks to...

Tutorial Author(s): Galo A. Goig, Daniela Brites, Christoph Stritt

Tutorial Contributor(s): Wolfgang Maier, Saskia Hiltemann, Helena Rasche, Galo A. Goig, Björn Grüning, Peter van Heusden, Christoph Stritt, Lucille Delisle

gtn star logo followed by the word workflows

Inputs

ID Name Description Type
Mycobacterium_tuberculosis_ancestral_reference.gbk #main/Mycobacterium_tuberculosis_ancestral_reference.gbk n/a
  • File
Paired-End FASTQs #main/Paired-End FASTQs n/a
  • array containing
    • File
Single-End FASTQs #main/Single-End FASTQs n/a
  • array containing
    • File

Steps

ID Name Description
3 Trimmomatic toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1
4 Trimmomatic toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1
5 Mapping and variant calling of SINGLE END FASTQs with snippy toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2
6 Mapping and variant calling of PAIRED END FASTQs with snippy toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/4.6.0+galaxy0
7 Merge PE/SE VCFs in a single collection with all samples __MERGE_COLLECTION__
8 Merge PE/SE BAMs in a single collection with all samples (Part the workflow "Identifying DR with TB-profiler) __MERGE_COLLECTION__
9 TB Variant Filter toolshed.g2.bx.psu.edu/repos/iuc/tb_variant_filter/tb_variant_filter/0.3.5+galaxy2

Outputs

ID Name Description Type
_anonymous_output_1 #main/_anonymous_output_1 n/a
  • File
_anonymous_output_10 #main/_anonymous_output_10 n/a
  • File
_anonymous_output_11 #main/_anonymous_output_11 n/a
  • File
_anonymous_output_2 #main/_anonymous_output_2 n/a
  • File
_anonymous_output_3 #main/_anonymous_output_3 n/a
  • File
_anonymous_output_4 #main/_anonymous_output_4 n/a
  • File
_anonymous_output_5 #main/_anonymous_output_5 n/a
  • File
_anonymous_output_6 #main/_anonymous_output_6 n/a
  • File
_anonymous_output_7 #main/_anonymous_output_7 n/a
  • File
_anonymous_output_8 #main/_anonymous_output_8 n/a
  • File
_anonymous_output_9 #main/_anonymous_output_9 n/a
  • File

Version History

1.0 (earliest) Created 2nd Jun 2025 at 10:59 by GTN Bot

Added/updated 4 files


Open master d00e09a
help Creators and Submitter
Creators
Not specified
Submitter
Discussion Channel
Activity

Views: 48   Downloads: 8   Runs: 0

Created: 2nd Jun 2025 at 10:59

help Attributions

None

Total size: 98 KB
Powered by
(v.1.17.0-main)
Copyright © 2008 - 2025 The University of Manchester and HITS gGmbH