A simple BASH script for identification of Streptococcus suis serotype from a draft genome

Database of serotype-specific sequences is modified from the SsuisSerotyping_pipeline (https://github.com/streplab/SsuisSerotyping_pipeline). Unlike the SsuisSerotyping_pipeline, the seroblast is dependent only on local blast installation.

1. install blast locally

for Ubuntu and Debian users

sudo apt install ncbi-blast+

others https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download

2. create /blastdb directory and put the file Ssuis_Serotyping8v2-NK-V2v3.fasta here

3. build blast database in /blastdb

makeblastdb -in Ssuis_Serotyping8v2-NK-V2v3.fasta -parse_seqids -blastdb_version 5 -title "SsuisSerotype" -dbtype nucl

4. edit line 5 in Ssuisseroblast8v2.NK-V2v4 script to locate the blast database in your correct path (for example /home/$HOME/blastdb) and make the script executable

chmod +x Ssuisseroblast8v2.NK-V2v4

5. run Ssuisseroblast8v2.NK-V2v4 from directory containing your S. suis draft genomes named *.fasta

./Ssuisseroblast8v2.NK-V2v4

7. read the output "serotypesV8v2.NK-V2v4.tsv" (tab separated columns). The columns are: "sample serotype cps_gene cps_evalue cps_score cps_ppos modifying_gene cps_evalue cps_score cps_ppos cpsk cpsk_evalue cpsk_score cpsk_ppos recN recN_evalue recN_score recN_ppos". As a modifying_gene, we understand a gene potentially able to modify antigenic structure of a capsular polysaccharide.