Description

Calling lowest common ancestors from multi-mapped reads in SAM/BAM/CRAM files

Input

Name (Type)
Description
Pattern

meta (map)

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

]

bam (file)

BAM/CRAM/SAM file

*.{bam,cram,sam}

bai (file)

BAM/CRAM/SAM index

*.{bai,.crai}

database (file)

Directory containing the sam2lca database

*

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

csv (file)

CSV file containing the sam2lca results

*.csv

json (file)

JSON file containing the sam2lca results

*.json

bam (file)

Optional sorted BAM/CRAM/SAM file annotated with LCA taxonomic informations

*.bam
author
Github user maxibor
get in touch
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Tools

sam2lca
GPL v3

Lowest Common Ancestor on SAM/BAM/CRAM alignment files

github.com/maxibor/sam2lca sam2lca.readthedocs.io 10.21105/joss.04360