This pipeline is designed to rapidly infer Streptococcus suis serotype from Oxford Nanopore data by first assemblying a draft genome using Flye followed by genome polishing with racon and medaka. The processed assembly is subsequently queried against the Cps Blast Database to determine isolate serotype. An additional variant calling step is employed to resolve serotype 2 and 1/2, as well as 1 and 14.

Required arguments:
-i  input file
-o  path to output directory
-s  sample name
-x  input type [fasta or fastq]

Optional arguments:
-h|--help       display help message
-t|--threads    number of threads [Default: 4]

Example Command Line:
SsuisSero.sh -s Sample_1 -i /path/to/Sample_1.fastq -o /path/to/output

The recommended method of installation for this pipeline is with Conda. Set up a new conda environment and run:

conda install -c bioconda ssuissero

• Medaka >= 1.0.1
• Freebayes >= 1.3.2
• Samtools >= 1.9
• Vcflib >= 1.0.0_rc2
• Blast >= 2.6
• Mummer = 3.23