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

]

reads (file)

Input Illunina paired-end FASTQ files

*.{fq.gz,fastq.gz}

Output

Name (Type)
Description
Pattern

meta (map)

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

versions (file)

File containing software versions

versions.yml

xml (file)

The predicted serotype in XML format

*.xml

txt (file)

A detailed description of the predicted serotype

*.txt

Tools

pneumocat
GPL v3

PneumoCaT (Pneumococcal Capsular Typing) uses a two-step step approach to assign capsular type to S.pneumoniae genomic data (Illumina)