README.md

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

v.1.0.4 is now broken on bioconda as picard is requesting now a higher java version. You can fix this by downgrading picard to a version smaller than 3. conda install picard=2.27.5

This has been fixed in the bioconda v.1.1.0 which should be available soon on bioconda.

Install Conda or Miniconda hereafter install MTBseq with:

conda install -c bioconda mtbseq

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)