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Source: seqsero
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
dh-python,
python3,
bwa,
sra-toolkit
Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/med-team/seqsero
Vcs-Git: https://salsa.debian.org/med-team/seqsero.git
Homepage: https://github.com/denglab/SeqSero
Rules-Requires-Root: no
Package: seqsero
Architecture: any
Depends: ${python3:Depends},
${misc:Depends},
python3-biopython,
bwa,
samtools,
sra-toolkit
Suggests: ispcr
Description: 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.
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