TBProfilerProfile Mycobacterium tuberculosis complex sequencing reads for lineage and known drug-resistance-associated variants. Processes one sample using the packaged who_v2+ mutation database and produces quality-control and resistance reports.Versions

v6.7.0 (default)

Tags: bioinformatics, tuberculosis, drug resistance, lineage typing, variant callingParameters

platform (enum) required: Sequencing platform. Use a single input read file for Nanopore or PacBio. Options: illumina, nanopore, pacbio

read1 (file) required: FASTQ reads for one sample: forward reads for paired-end Illumina data, or the single read file for single-end or long-read data.

read2 (file): Matching reverse reads for paired-end Illumina data. Leave empty for single-end, Nanopore or PacBio input.

Links

License: GPL-3.0-or-later

Cite as: Phelan JE, O’Sullivan DM, Machado D, et al. (2019). Integrating informatics tools and portable sequencing technology for rapid detection of resistance to anti-tuberculous drugs. *Genome Medicine* 11, 41. https://doi.org/10.1186/s13073-019-0650-x

Open TBProfiler in the CPG Portal. Configuring and running a tool needs JavaScript.