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 (map)

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

]

fasta (file)

Reference genome

*.{fasta}

Output

Name (Type)
Description
Pattern

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

list (file)

File containing microsatellite list

*.{list}
included in
sarek
maintainer
Github user FriederikeHanssen
get in touch
Ask a question on Slack Open an issue on GitHub

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