Calling lowest common ancestors from multi-mapped reads in SAM/BAM/CRAM files
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
bam{:bash}
:file
BAM/CRAM/SAM file
*.{bam,cram,sam}
bai{:bash}
BAM/CRAM/SAM index
*.{bai,.crai}
database{:bash}
Directory containing the sam2lca database
*
csv{:bash}
*.csv{:bash}
CSV file containing the sam2lca results
*.csv
json{:bash}
*.json{:bash}
JSON file containing the sam2lca results
*.json
*.bam{:bash}
Optional sorted BAM/CRAM/SAM file annotated with LCA taxonomic information
*.bam
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
Lowest Common Ancestor on SAM/BAM/CRAM alignment files
