Package: seqsero (1.0.1+dfsg-1)

[ Source: seqsero  ]

Salmonella serotyping from genome sequencing data

SeqSero is a pipeline for Salmonella serotype determination from raw sequencing reads or genome assemblies.

SeqSero is a novel tool for determining Salmonella serotypes using high- throughput genome sequencing data. SeqSero is based on curated databases of Salmonella serotype determinants (rfb gene cluster, fliC and fljB alleles) and is predicted to determine serotype rapidly and accurately for nearly the full spectrum of Salmonella serotypes (more than 2,300 serotypes), from both raw sequencing reads and genome assemblies. The performance of SeqSero was evaluated by testing

 1. raw reads from genomes of 308 Salmonella isolates of known serotype
 2. raw reads from genomes of 3,306 Salmonella isolates sequenced and
    made publicly available by GenomeTrakr, a U.S. national monitoring
    network operated by the Food and Drug Administration; and
 3. 354 other publicly available draft or complete Salmonella genomes.

SeqSero can help to maintain the well-established utility of Salmonella serotyping when integrated into a platform of WGS-based pathogen subtyping and characterization.

Other Packages Related to seqsero

• dep: bwa

  Burrows-Wheeler Aligner

• dep: python

  interactive high-level object-oriented language (Python2 version)

• dep: python-biopython

  Python library for bioinformatics (implemented in Python 2)

• dep: samtools

  processing sequence alignments in SAM, BAM and CRAM formats

• dep: sra-toolkit

  utilities for the NCBI Sequence Read Archive

• sug: ispcr

  Package not available

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