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Repository tbprofiler

Name: tbprofiler

Owner: iuc

Synopsis: Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers.

Detailed description:

This repository contains a complete rewrite of the web version of TBProfiler, described here.
It allows the use of profiling through a command line interface and contains some additional
functionality such as the ability to process minION data.

The pipeline aligns reads to the H37Rv reference using bowtie2, BWA or minimap2
and then calls variants using SAMtools. These variants are then compared to a
drug-resistance database. We also predict the number of reads supporting drug
resistance variants as an insight into hetero-resistance (not applicable for minION data)

Full documentation at https://github.com/jodyphelan/TBProfiler

Content homepage: https://github.com/jodyphelan/TBProfiler

Development repository: https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler

Link to this repository: https://toolshed.g2.bx.psu.edu/view/iuc/tbprofiler/809dfc93d593

Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/tbprofiler

Type: unrestricted

Revision: 13:809dfc93d593

This revision can be installed: True

Times cloned / installed: 493