From BAMs to drug resistance prediction with TB-profiler

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Workflow Type: Galaxy

Starting from the BAM files produced by snippy, generate a table that summarizes the drug-resistance profile for each sample

Associated Tutorial

This workflows is part of the tutorial From BAMs to drug resistance prediction with TB-profiler, available in the GTN

Thanks to...

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

Tutorial Contributor(s): Wolfgang Maier

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1314?version=2

Inputs

ID Name Description Type
MTB paired-end BAMs #main/MTB paired-end BAMs BAMs obtained from paired-end mappings with snippy
  • array containing
    • File
MTB single-end BAMs #main/MTB single-end BAMs BAMs obtained from single-end mappings with snippy
  • array containing
    • File

Steps

ID Name Description
2 Merge collections Merge single-end and paired-end BAMs in a single collection to be analyzed alltogether __MERGE_COLLECTION__
3 Samtools view BAM > SAM We want a text (SAM) file to substitute the string "MTB_anc" by "Chromosome" so it is compatible with TB-profiler toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.13+galaxy2
4 Sed (MTB_anc to Chromosome) Change the string MTB_anc to "Chromosome" so it is compatible with TB-profiler toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1
5 Samtools view SAM > BAM toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.13+galaxy2
6 TB-profiler Generate TB-profiler reports with drug resistance determinants toolshed.g2.bx.psu.edu/repos/iuc/tbprofiler/tb_profiler_profile/3.0.8+galaxy0
7 Get drug resistance profile From TB profiler, search with `grep` the part of the text that describes the DR profile (e.g Drug-Resistance: MDR) toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1
8 Add Sample Name We have generated one file per sample, that contains the DR profile (e.g Drug-Resistance: MDR) We want to prepend the name of the sample so we have: (Sample_name Drug-Resistance: MDR) toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0
9 Concatenate DR profiles in a single table The output will be: Sample_A DR_profile_A Sample_B DR_profile_B Sample_Z DR_profile_Z toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1
10 Cleanup the table Remove unnecessary text from the table like ".txt" or "Drug-resistance:" toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2

Outputs

ID Name Description Type
Samtools view on input dataset(s): filtered alignments #main/Samtools view on input dataset(s): filtered alignments n/a
  • File
_anonymous_output_1 #main/_anonymous_output_1 n/a
  • File
_anonymous_output_10 #main/_anonymous_output_10 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 (latest) Created 16th Jul 2024 at 14:24 by Helena Rasche

Added/updated 4 files


Open master d7b26d2

2.0 (earliest) Created 25th Jun 2024 at 11:23 by Helena Rasche

Added/updated 4 files


Frozen 2.0 bf8ec3c
help Creators and Submitter
Creators
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Submitter
Discussion Channel
GTN Matrix
Tools
SAMtools
tb-profiler
License
Creative Commons Attribution 4.0 International
Activity

Views: 607   Downloads: 179

Created: 25th Jun 2024 at 11:23

Last updated: 25th Jun 2024 at 11:23

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