lima - The PacBio Barcode Demultiplexer and Primer Remover
meta:map
Groovy Map containing sample information e.g. [ id:‘test’ ]
ccs:file
A BAM or fasta or fasta.gz or fastq or fastq.gz file of subreads or ccs
*.{bam,fasta,fasta.gz,fastq,fastq.gz}
primers:file
Fasta file, sequences of primers
*.fasta
counts
*.counts:file
A tabulated file of describing pairs of primers
*.counts
report
*.report:file
A tab-separated file about each ZMW, unfiltered
*.report
summary
*.summary:file
This file shows how many ZMWs have been filtered, how ZMWs many are same/different, and how many reads have been filtered.
*.summary
versions
versions.yml:file
File containing software versions
versions.yml
bam
*.bam:file
A bam file of ccs purged of primers
*.bam
pbi
*.bam.pbi:file
Pacbio index file of ccs purged of primers
fasta
*.{fa, fasta}:file
A fasta file of ccs purged of primers.
*.fa
fastagz
*.{fa.gz, fasta.gz}:file
A fasta.gz file of ccs purged of primers.
*.fasta.gz
fastq
*.fastq:file
A fastq file of ccs purged of primers.
*.fastq
fastqgz
*.fastq.gz:file
A fastq.gz file of ccs purged of primers.
*.fastq.gz
xml
*.xml:file
An XML file representing a set of a particular sequence data type such as subreads, references or aligned subreads.
*.xml
json
*.json:file
A metadata json file
*.json
clips
*.clips:file
A fasta file of clipped primers
*.clips
guess
*.guess:file
A second tabulated file of describing pairs of primers (no doc available)
*.guess
