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:false ]

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:false ]

*.csv:file

CSV file containing the sam2lca results

*.csv

json

meta:map

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

*.json:file

JSON file containing the sam2lca results

*.json

bam

meta:map

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

*.bam:file

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

*.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
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