Description

Use deamination patterns to estimate contamination in single-stranded libraries

Input

Name (Type)
Description
Pattern

meta (map)

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

]

bam (file)

BAM/CRAM/SAM file (Mandatory)

*.{bam,cram,sam}

config (file)

Optional AuthentiCT configuration text file

*

positions (file)

Optional text file with positions that sequences should overlap

*

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

txt (file)

Maximum likelihood estimates with associated standard errors

*.txt
maintainers
Github user scarlhoff
Github user StephanePeyregne
get in touch
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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