Description

Remove polyA tail and artificial concatemers

Input

Name (Type)
Description
Pattern

meta (map)

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

bam (file)

BAM file, cleaned ccs generated by lima

*.bam

primers (file)

fasta file of primers

*.fasta

Output

Name (Type)
Description
Pattern

meta (map)

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

bam (file)

Set of complete reads (with polyA tail), where the polyA has been trimmed

*.bam

pbi (file)

Pacbio index file from polyA trimmed reads

*.pbi

consensusreadset (file)

Metadata about read library

*.xml

summary (file)

json file describing number of full length reads, full length non chimeric reads and full length non chimeric polyA reads

*.json

report (file)

Metadata about primer and polyA detection (primers/polyA/insert length, strand, primer name)

*.csv

versions (file)

File containing software versions

versions.yml
included in
isoseq
author
Github user sguizard
get in touch
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Tools

isoseq3
BSD-3-Clause-Clear

IsoSeq3 - Scalable De Novo Isoform Discovery

github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md