Input
Name (Type)
Description
Pattern
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
*.{fq,fastq,fq.gz,fastq.gz}
Output
Name (Type)
Description
Pattern
The alignments in BAM format. Includes unmapped, multimapping reads. Excludes duplicates.
*.bam
A version of the reference but with - at position with depth=0 and N for 0 < depth < —mincov (does not have variants)
*.aligned.fa
A version of the reference genome with only substitution variants instantiated
*.consensus.subs.fa