Description

msisensor2 detection of MSI regions.

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

fasta:file

Reference genome

*.{fasta}

Output

name:type
description
pattern

scan

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.scan:file

File containing microsatellite list

*.{scan}

versions

versions.yml:file

File containing software versions

versions.yml

Tools

msisensor2
GPL-3.0

MSIsensor2 is a novel algorithm based machine learning, featuring a large upgrade in the microsatellite instability (MSI) detection for tumor only sequencing data, including Cell-Free DNA (cfDNA), Formalin-Fixed Paraffin-Embedded(FFPE) and other sample types. The original MSIsensor is specially designed for tumor/normal paired sequencing data.

github.com/niu-lab/msisensor2 github.com/niu-lab/msisensor2/blob/master/README.md https://github.com/niu-lab/msisensor2
maintainer
Github user adamrtalbot
get in touch
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