Description

Bayesian reconstruction of ancient DNA fragments

Input

Name (Type)
Description
Pattern

meta (map)

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

]

reads (file)

Unaligned BAM or one or two gzipped FASTQ file(s)

*.{bam,fq.gz,fastq.gz}

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

bam (file)

BAM file

*.bam

fq_pass (file)

Trimmed and merged FASTQ

*.fq.gz

fq_fail (file)

Failed trimmed and merged FASTQs

*.fail.fq.gz

unmerged_r1_fq_pass (file)

Passed unmerged R1 FASTQs

*.r1.fq.gz

unmerged_r1_fq_fail (file)

Failed unmerged R1 FASTQs

*.r1.fail.fq.gz

unmerged_r2_fq_pass (file)

Passed unmerged R2 FASTQs

*.r2.fq.gz

unmerged_r2_fq_pass (file)

Failed unmerged R2 FASTQs

*.r2.fail.fq.gz

log (file)

Log file of command

*.log
author
Github user jfy133
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Tools

leehom
GPL v3

Bayesian reconstruction of ancient DNA fragments

grenaud.github.io/leeHom github.com/grenaud/leeHom 10.1093/nar/gku699