Mycobacterium tuberculosis

Usage

The workflow intended for analysis of species that are part of the Mycobacterium tuberculosis complex.

Supported analysis

The workflow includes the following analysis in addition to species prediction and various methods for assessing the sequencing quality,

  • Antibiotic resistance prediction

Software versions

Versions of softwares and containers used by the Mycobacterium tuberculosis workflow.

Software

Version

Container

bracken

2.8

https://depot.galaxyproject.org/singularity/bracken:2.8–py39hc16433a_0

bwa

0.7.17-r1188

https://depot.galaxyproject.org/singularity/bwakit:0.7.17.dev1–hdfd78af_1

filtlong

0.3.1

https://depot.galaxyproject.org/singularity/filtlong:0.3.1–h077b44d_0

flye

2.9.6

https://depot.galaxyproject.org/singularity/flye:2.9.6–py39h475c85d_0

hostile

2.0.0

https://depot.galaxyproject.org/singularity/hostile:2.0.0–pyhdfd78af_0

minimiap2

2.30

https://depot.galaxyproject.org/singularity/minimap2:2.30–h577a1d6_0

medaka

2.2.0

docker://ontresearch/medaka:shacf8338462607b17b1d68dbce212cb93daea50bad

mykrobe

0.12.2

https://depot.galaxyproject.org/singularity/mykrobe:0.12.2–py39h70e0db4_0

nanoplot

1.46.2

https://depot.galaxyproject.org/singularity/nanoplot:1.46.2–pyhdfd78af_0

prp

1.6.1

docker://clinicalgenomicslund/bonsai-prp:1.6.1

quast

5.2.0

https://depot.galaxyproject.org/singularity/quast:5.2.0–py310pl5321hc8f18ef_2

samtools

1.17

https://depot.galaxyproject.org/singularity/samtools:1.17–h00cdaf9_0

seqtk

1.4

https://depot.galaxyproject.org/singularity/seqtk:1.4–he4a0461_2

ska2

0.3.10

https://depot.galaxyproject.org/singularity/ska2:0.3.10–h4349ce8_0

skesa

2.5.1

https://depot.galaxyproject.org/singularity/skesa:2.5.1–hdcf5f25_0

snippy

4.6.0

https://depot.galaxyproject.org/singularity/snippy:4.6.0–hdfd78af_2

sourmash

4.8.2

https://depot.galaxyproject.org/singularity/sourmash:4.8.2–hdfd78af_0

tb-profiler

6.7.0

https://depot.galaxyproject.org/singularity/tb-profiler:6.7.0–pyhdfd78af_0

trimmomatic

0.40

https://depot.galaxyproject.org/singularity/trimmomatic:0.40–hdfd78af_0