Description

Conversion of PacBio BAM files into gzipped fastq files, including splitting of barcoded data

Input

Name (Type)
Description
Pattern

meta (map)

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

]

bam (file)

PacBio BAM file

*.bam

index (file)

PacBio BAM file index (.pbi)

*.pbi

Output

Name (Type)
Description
Pattern

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

fastq (file)

Gzipped FASTQ file

*.fastq.gz
maintainers
Github user priyanka-surana
Github user muffato
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

bam2fastx
BSD-3-clause-Clear

Converting and demultiplexing of PacBio BAM files into gzipped fasta and fastq files

github.com/PacificBiosciences/bam2fastx