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

csv

meta:map

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

]

*.csv:file

CSV file containing the sam2lca results

*.csv

json

meta:map

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

]

*.json:file

JSON file containing the sam2lca results

*.json

bam

meta:map

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

]

*.bam:file

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

*.bam

versions

versions.yml:file

File containing software versions

versions.yml

Tools

sam2lca
GPL v3

Lowest Common Ancestor on SAM/BAM/CRAM alignment files

github.com/maxibor/sam2lca sam2lca.readthedocs.io 10.21105/joss.04360
maintainer
Github user maxibor
get in touch
Ask a question on Slack Open an issue on GitHub