Calling lowest common ancestors from multi-mapped reads in SAM/BAM/CRAM files
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
*
csv
*.csv:file
CSV file containing the sam2lca results
*.csv
json
*.json:file
JSON file containing the sam2lca results
*.json
bam
*.bam:file
Optional sorted BAM/CRAM/SAM file annotated with LCA taxonomic information
*.bam
versions
versions.yml:file
File containing software versions
versions.yml
Lowest Common Ancestor on SAM/BAM/CRAM alignment files
