Description

PRINSEQ++ is a C++ implementation of the prinseq-lite.pl program. It can be used to filter, reformat or trim genomic and metagenomic sequence data

Input

name:type
description
pattern

meta:map

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

reads:file

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

Output

name:type
description
pattern

good_reads

meta:map

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

*_good_out*.fastq.gz:file

Reads passing filter(s) in gzipped FASTQ format

*_good_out_{R1,R2}.fastq.gz

single_reads

meta:map

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

*_single_out*.fastq.gz:file

Single reads without the pair passing filter(s) in gzipped FASTQ format

*_single_out_{R1,R2}.fastq.gz

bad_reads

meta:map

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

*_bad_out*.fastq.gz:file

Reads without not passing filter(s) in gzipped FASTQ format

*_bad_out_{R1,R2}.fastq.gz

log

meta:map

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

*.log:file

Verbose level 2 STDOUT information in a log file

*.log

versions

versions.yml:file

File containing software versions

versions.yml

Tools

prinseqplusplus
GPL v2

PRINSEQ++ - Multi-threaded C++ sequence cleaning

github.com/Adrian-Cantu/PRINSEQ-plus-plus 10.7287/peerj.preprints.27553v1
taxprofiler
Github user jfy133
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