Determine Streptococcus pneumoniae serotype from Illumina paired-end reads
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}
xml
Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
[ id:'test', single_end:false ]
*.xml:file
The predicted serotype in XML format
*.xml
txt
*.txt:file
A detailed description of the predicted serotype
*.txt
versions
versions.yml:file
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)
