Description

IsoSeq3 - Cluster - Cluster trimmed consensus sequences

Input

name:type
description
pattern

meta:map

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

bam:file

BAM file generated by isoseq3 refine

*.bam

Output

name:type
description
pattern

meta:map

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

]

version:file

File containing software version

versions.yml

bam:file

BAM file of clustered consensus

*.transcripts.bam

pbi:file

Pacbio Index of consensus reads generated by clustering

*.transcripts.bam.pbi

cluster:file

A two columns (from, to) file describing original read name to new read name

*.transcripts.cluster

cluster_report:file

A table files clusters (transcripts) members (read)

*.transcripts.cluster_report.csv

transcriptset:file

A metadata xml file which contains full paths to data files

*.transcripts.transcriptset.xml

hq_bam:file

High quality reads (when —use-qvs is set)

*.transcripts.hq.bam

hq_pbi:file

Pacbio index of high quality reads (when —use-qvs is set)

*.transcripts.hq.bam.pbi

lq_bam:file

Low quality reads (when —use-qvs is set)

*.transcripts.lq.bam

lq_pbi:file

Pacbio index of low quality reads (when —use-qvs is set)

*.transcripts.lq.bam.pbi

singletons_bam:file

Unclustered reads (when —singletons is set)

*.transcripts.singletons.bam

singletons_pbi:file

Pacbio index of unclustered reads (when —singletons is set)

*.transcripts.singletons.bam.pbi

Tools

isoseq3
BSD-3-Clause-Clear

IsoSeq3 - Cluster - Cluster trimmed consensus sequences