MTBseq

MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from Illumina whole genome sequence data of Mycobacterium tuberculosis complex isolates.

Getting Started

For complete installation instructions, description and usage examples please read the MANUAL.md.

Installation

Conda

Install Conda or Miniconda hereafter install MTBseq with:

conda install -c bioconda mtbseq

Due to license restrictions, even bioconda cannot install the dependency GenomeAnalysisTK 3.8 directly. After installation of MTBseq to fully install the GATK, you must download a licensed copy of the GenomeAnalysisTK 3.8 from the Broad Institute (https://console.cloud.google.com/storage/browser/gatk-software/package-archive/gatk). For direct download from the commandline: wget https://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.8-0-ge9d806836.tar.bz2

To register call:

gatk3-register /path/to/GenomeAnalysisTK[-$PKG_VERSION.tar.bz2|.jar]

, which will copy GATK into your conda environment.

Source

Please see the MANUAL.md for installation from source.

Requirements

* Perl: Perl 5, version 22, subversion 1 (v5.22.1)
* Java: Oracle Java 8 or OpenJDK 8 (no other version work with the GenomeAnalysisTK 3.8)

** MTBseq uses the following CPAN and core modules: **
* MCE                 (v1.833)
* Statistics::Basic   (v1.6611)

* FindBin             (v1.51)core
* Cwd                 (v3.62)core
* Getopt::Long        (v2.5)core
* File::Copy          (v2.30)core
* List::Util          (v1.49)core
* Exporter            (v5.72)core
* vars                (v1.03)core
* lib                 (v0.63)core
* strict              (v1.09)core
* warnings            (v1.34)core

** MTBseq uses the following third party software: **
** Binaries (compiled on Ubuntu 16.04) are included, except for GenomeAnalysisTK 3.8**
* bwa                 (v0.7.17)
* GenomeAnalysisTK    (v3.8)
* picard              (v2.17.0)
* samtools            (v1.6)