modules/pbccs

Pacbio ccs - Generate Highly Accurate Single-Molecule Consensus Reads

ccspacbioisoseqsubreads

https://github.com/nf-core/modules/[...]/modules/nf-core/pbccs

Description

Pacbio ccs - Generate Highly Accurate Single-Molecule Consensus Reads

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information id: id of the split file

`bam`
`:file`

Raw subreads bam

*.subreads.bam

`pbi`
`:file`

Pacbio BAM Index

*.pbi

`chunk_num`
`:integer`

BAM part to process

`chunk_on`
`:integer`

Total number of bam parts to process

Output

name:type

description

pattern

`bam`

`meta`
`:map`

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

`.chunk.bam`
`:file`

CCS sequences in bam format

*.bam

`pbi`

`meta`
`:map`

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

`.chunk.bam.pbi`
`:file`

PacBio Index of CCS sequences

*.pbi

`report_txt`

`meta`
`:map`

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

`*.report.txt`
`:file`

CCS report in text format

*.report.txt

`report_json`

`meta`
`:map`

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

`*.report.json`
`:file`

CCS report in JSON format

*.report.json

`metrics`

`meta`
`:map`

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

`*.metrics.json.gz`
`:file`

Metrics about zmws

*.json.gz

`versions`

`versions.yml`
`:file`

File containing software versions

versions.yml

Tools

pbccs
BSD-3-Clause-Clear

pbccs - Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)

github.com/PacificBiosciences/pbbioconda ccs.how https://github.com/PacificBiosciences/ccs