Description

Short Read Sequence Typing for Bacterial Pathogens is a program designed to take Illumina sequence data, a MLST database and/or a database of gene sequences (e.g. resistance genes, virulence genes, etc) and report the presence of STs and/or reference genes.

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information id: should be the identification number or sample name single_end: should be true for single end data and false for paired in data db: should be either ‘gene’ to use the —gene_db option or “mlst” to use the —mlst_db option e.g. [ id:‘sample’, single_end

, db:‘gene’]

fastq_s:file

input FastQ files

*.{fq,fastq,fq.gz,fastq.gz}

db:file

Database in FASTA format

*.fasta

Output

name:type
description
pattern

gene_results

meta:map

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

]

*_genes_*_results.txt:file

SRST2 gene results

*_genes_*_results.txt

fullgene_results

meta:map

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

]

*_fullgenes_*_results.txt:file

SRST2 full gene results

*_fullgenes_*_results.txt

mlst_results

meta:map

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

]

*_mlst_*_results.txt:file

SRST2 MLST results

*_mlst_*_results.txt

pileup

meta:map

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

]

*.pileup:file

SAMtools pileup file

*.pileup

sorted_bam

meta:map

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

]

*.sorted.bam:file

Sorted BAM file

*.sorted.bam

versions

versions.yml:file

File containing software versions

versions.yml

Tools

maintainer
Github user jvhagey
get in touch
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