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Scope
Will Pitchers edited this page Apr 15, 2019
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The scripts in this repository are to be used to perform in silico serotyping of Salmonella enterica in accordance with MMS136. This pipeline allows us to infer the Salmonella serovar; replacing phenotypic serotyping while ensuring backwards compatibility with historical typing data (on the White-Kauffman-Le Minor scheme), and continuity in public health surveillance.
This pipeline takes as input a draft assembly and outputs a serotype inference. The draft assembly is obtained by performing a de novo assembly on FASTQ data found to have passed MMS103 and to be identified as Salmonella enterica by kmer ID and by a wet laboratory method.
| SOP | Title |
|---|---|
| MMS103 | Whole Genome Sequencing |
| ENS003 | Salmonella – Biochemical tests and identification |
| ENS005 | Salmonella O Antigen Testing |
| ENS010 | Salmonella H Antigen Testing |
| ENS006 | Salmonella-Testing Rough Strains |
| MMS001 | DNA extraction and nucleic acid amplification |
| MMS125 | Operation and maintenance of the Qiasymphony |
| MMS104 | Detection of Salmonella typhimurium by RT-PCR |
| BIS001 | Read data quality control |
Reviewed by Anders Goncalves da Silva on 2019-06-21