Description

Use deamination patterns to estimate contamination in single-stranded libraries

Input

name:type
description
pattern

meta{:bash}

:map

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

bam{:bash}

:file

BAM/CRAM/SAM file (Mandatory)

*.{bam,cram,sam}

meta2{:bash}

:map

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

config{:bash}

:file

Optional AuthentiCT configuration text file

*

meta3{:bash}

:map

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

positions{:bash}

:file

Optional text file with positions that sequences should overlap

*

Output

name:type
description
pattern

txt{:bash}

meta{:bash}

:map

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

*.txt{:bash}

:file

Maximum likelihood estimates with associated standard errors

*.txt

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

authentict
GPL v3

Estimates present-day DNA contamination in ancient DNA single-stranded libraries.

github.com/StephanePeyregne/AuthentiCT 10.1186/s13059-020-02123-y
maintainers
Github user scarlhoff
Github user StephanePeyregne
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