Description

Split sequencing reads by mapping them to multiple references simultaneously

Input

Name (Type)
Description
Pattern

meta (map)

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

]

reads (file)

List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.

index (directory)

Directory to place generated index

*

primary_ref (file)

Path to the primary reference

*

other_ref_names (list)

List of other reference ids apart from the primary

other_ref_paths (list)

Path to other references paths corresponding to “other_ref_names”

only_build_index (string)

true = only build index; false = mapping

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

index (directory)

Directory with index files

bbsplit

primary_fastq (file)

Output reads that map to the primary reference

*primary*fastq.gz

all_fastq (file)

All reads mapping to any of the references

*fastq.gz

stats (file)

Tab-delimited text file containing mapping statistics

*.txt
included in
rnaseq
authors
Github user joseespinosa Github user drpatelh
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

bbmap
UC-LBL license (see package)

BBMap is a short read aligner, as well as various other bioinformatic tools.

jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide