Mtb Common Drug Mutations Discovery

Overview

This repository focuses on UG sub-lineage mutations and drug resistance mutation discovery for Mycobacterium tuberculosis (MTB). It leverages tools like FastQC, MultiQC, and Snippy for rapid bacterial SNP genotype and drug resistance calling (Version 1.0.0).

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Author

Gerald Mboowa

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Synopsis

Snippy identifies SNPs between a haploid reference genome and HTS datasets. It detects both substitutions (SNPs) and insertions/deletions (indels). Snippy is designed for speed and efficiency, supporting multi-threading on a single machine. It produces consistent output files in a single folder. (Tested with Snippy 4.3.2 - Torsten Seemann's Snippy).

Key Tools:

1. FastQC
   Provides quality control checks on raw sequence data from high-throughput sequencing pipelines.

2. MultiQC
   Aggregates analysis logs into a single HTML report, summarizing outputs from multiple tools like FastQC.

3. Snippy
   Processes samples for SNP discovery and annotation.

4. MTB Genotypes and Drug Resistance Annotations
   Identifies MTB sub-lineages and drug resistance mutations, including MDR and XDR strains.

5. Redundant File Cleanup
   Deletes unnecessary files generated during the pipeline execution.

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Output Files

The pipeline generates the following output files:

• Text files detailing MTB genotypes
• Text files summarizing drug resistance mutations for both MDR and XDR strains

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Issues

For suggestions or to report bugs, please use the Issue Tracker.

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Requirements

Software

• FastQC
• MultiQC
• Perl (>= 5.12)
  • Modules: Time::Piece (core with modern Perl), Bioperl (>= 1.6)
• BWA MEM (>= 0.7.12)
• Minimap2 (>= 2.0)
• Samtools (>= 1.7)
• Bedtools (>= 2.0)
• BCFtools (>= 1.7)
• GNU Parallel (>= 2013xxxx)
• FreeBayes (>= 1.1)
  • Includes: freebayes, freebayes-parallel, fasta_generate_regions.py
• VCFtools (vcflib) (>= 1.0)
  • Includes: vcfstreamsort, vcfuniq, vcffirstheader
• VT (>= 0.5)
• ReadSeq (>= 2.0)
• SnpEff (>= 4.3)
• Samclip (>= 0.2)
• Seqtk (>= 1.2)
• Snp-Sites (>= 2.0)
• Wgsim (>= 1.8) (for testing only)

Bundled Binaries

This pipeline has been tested on macOS Mojave using precompiled binaries.

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Disclaimer

Ensure the listed dependencies are properly installed and configured before running the pipeline. Refer to the respective tool documentation for detailed installation and usage guidelines.

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Contact

For further inquiries or collaborations, please contact the author.