Description

lima - The PacBio Barcode Demultiplexer and Primer Remover

Input

Name (Type)
Description
Pattern

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

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’ ]

bam (file)

A bam file of ccs purged of primers

*.bam

pbi (file)

Pacbio index file of ccs purged of primers

*.bam

xml (file)

An XML file representing a set of a particular sequence data type such as subreads, references or aligned subreads.

*.xml

json (file)

A metadata json file

*.json

clips (file)

A fasta file of clipped primers

*.clips

counts (file)

A tabulated file of describing pairs of primers

*.counts

guess (file)

A second tabulated file of describing pairs of primers (no doc available)

*.guess

report (file)

A tab-separated file about each ZMW, unfiltered

*.report

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

fasta (file)

A fasta file of ccs purged of primers.

*.fa

fastagz (file)

A fasta.gz file of ccs purged of primers.

*.fasta.gz

fastq (file)

A fastq file of ccs purged of primers.

*.fastq

fastqgz (file)

A fastq.gz file of ccs purged of primers.

*.fastq.gz

versions (file)

File containing software versions

versions.yml

Tools

lima
BSD-3-Clause-Clear

lima - The PacBio Barcode Demultiplexer and Primer Remover