Description

Compares query sketches to reference sketches hosted on a remote server via the Internet.

Input

name:type
description
pattern

meta{:bash}

:map

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

file{:bash}

:file

file with nucleotide sequences

*.{fna, fa, fasta, fa.gz, fasta.gz, fna.gz, fastq.gz, fastq, fq.gz, fq}

Output

name:type
description
pattern

hits{:bash}

meta{:bash}

:map

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

*.txt{:bash}

:file

.txt file containing hits from a query seuqnce to various reference sequences output

*.{txt}

versions_bbmap{:bash}

${task.process}{:bash}

:string

The name of the process

bbmap{:bash}

:string

The name of the tool

bbversion.sh | grep -v "Duplicate cpuset"{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

bbmap{:bash}

:string

The name of the tool

bbversion.sh | grep -v "Duplicate cpuset"{:bash}

:eval

The expression to obtain the version of the tool

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/software-tools/bbtools/bb-tools-user-guide
included in
pathogensurveillance
maintainer
Github user phanhung2
get in touch
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