recipe mtbseq

Pipeline for WGS analysis of M. tuberculosis

Homepage

https://github.com/ngs-fzb/MTBseq_source

License

GPLv3

Recipe

/mtbseq/meta.yaml

MTBseq is a semi-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

package mtbseq

Versions

1.0.4-0,  1.0.3-1,  1.0.3-0

Depends

• bwa 0.7.17

• gatk 3.8

• openjdk >=8,<9

• perl >=5.26.2,<5.26.3.0a0

• perl-mce >=1.836

• perl-number-format

• perl-statistics-basic >=1.6611

• picard >=2.17.0

• samtools 1.6

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install mtbseq

and update with:

conda update mtbseq

or use the docker container:

docker pull quay.io/biocontainers/mtbseq:<tag>

(see mtbseq/tags for valid values for <tag>)

Link to this page

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