Determine Streptococcus pneumoniae serotype from Illumina paired-end reads
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
reads{:bash}
:file
Input Illunina paired-end FASTQ files
*.{fq.gz,fastq.gz}
xml{:bash}
Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
[ id:'test', single_end:false ]
*.xml{:bash}
The predicted serotype in XML format
*.xml
txt{:bash}
*.txt{:bash}
A detailed description of the predicted serotype
*.txt
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
PneumoCaT (Pneumococcal Capsular Typing) uses a two-step step approach to assign capsular type to S.pneumoniae genomic data (Illumina)
