Description

MSIsensor-pro evaluates Microsatellite Instability (MSI) for cancer patients with next generation sequencing data. It accepts the whole genome sequencing, whole exome sequencing and target region (panel) sequencing data as input

Input

name:type
description
pattern

meta{:bash}

:map

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

fasta{:bash}

:file

Reference genome

*.{fasta}

Output

name:type
description
pattern

list{:bash}

meta{:bash}

:map

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

*.list{:bash}

:file

File containing microsatellite list

*.{list}

versions_msisensorpro{:bash}

${task.process}{:bash}

:string

The name of the process

msisensor-pro{:bash}

:string

The name of the tool

msisensor-pro --version 2>&1 | sed -nE 's/Version:\s*//p'{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

msisensor-pro{:bash}

:string

The name of the tool

msisensor-pro --version 2>&1 | sed -nE 's/Version:\s*//p'{:bash}

:eval

The expression to obtain the version of the tool

Tools

msisensorpro
Custom Licence

Microsatellite Instability (MSI) detection using high-throughput sequencing data.

github.com/xjtu-omics/msisensor-pro github.com/xjtu-omics/msisensor-pro/wiki https://github.com/xjtu-omics/msisensor-pro 10.1016/j.gpb.2020.02.001
included in
referencessarek
maintainer
Github user FriederikeHanssen
get in touch
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