Advanced sequence file format conversions
meta
Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
reads
BAM/CRAM/SAM file
*.{bam,cram,sam}
fasta
Reference genome in FASTA format
*.{fa,fasta}
fai
FASTA index file from samtools faidx
*.{fai}
gzi
Optional gzip index file for BAM inputs
*.gzi
versions
File containing software versions
versions.yml
Converted reads
*.{sam, bam, cram}
gzip index file for BAM outputs
.{bam.gzi}
Staden Package 'io_lib' (sometimes referred to as libstaden-read by distributions). This contains code for reading and writing a variety of Bioinformatics / DNA Sequence formats.