Description

Determine Streptococcus pneumoniae serotype from Illumina paired-end reads

Input

name:type
description
pattern

meta:map

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

reads:file

Input Illunina paired-end FASTQ files

*.{fq.gz,fastq.gz}

Output

name:type
description
pattern

tsv

meta:map

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

${prefix}/${prefix}.tsv:file

The predicted serotype in tab-delimited format

*.tsv

txt

meta:map

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

${prefix}/detailed_serogroup_info.txt:file

A detailed description of the predicted serotype

*.txt

versions

versions.yml:file

File containing software versions

versions.yml

Tools

seroba
GPL v3

SeroBA is a k-mer based pipeline to identify the Serotype from Illumina NGS reads for given references.