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SeqSero specifications

Information


Unique identifier OMICS_21700
Name SeqSero
Interface Web user interface
Restrictions to use None
Input format FASTQ, SRA
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Xiangyu Deng

Additional information


https://github.com/denglab/SeqSero

Information


Unique identifier OMICS_21700
Name SeqSero
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl, Python
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Versioning


No version available

Maintainer


  • person_outline Xiangyu Deng

Additional information


https://github.com/denglab/SeqSero

Publication for SeqSero

SeqSero citations

 (20)
library_books

Draft Genome Sequences of Two Salmonella Strains Isolated from Wild Animals on the Eastern Shore of Virginia

2018
Genome Announc
PMCID: 5946047
PMID: 29748400
DOI: 10.1128/genomeA.00329-18

[…] sion 2 according to the manufacturer's instructions.The serotypes of each strain (VA-WGS-00333: Weslaco; VA-WGS-00353: Singapore) were verified using the in silico Salmonella serotype prediction tool SeqSero version 1.0 (). De novo assemblies were generated using SPAdes version 3.9.0 (), and annotation of the draft genomes was performed using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) […]

library_books

A Comparative Genomic Analysis Provides Novel Insights Into the Ecological Success of the Monophasic Salmonella Serovar 4,[5],12:i:

2018
Front Microbiol
PMCID: 5913373
PMID: 29719530
DOI: 10.3389/fmicb.2018.00715

[…] ing from sample annotation. The sample was considered for subsequent analysis when these metrics fell in a range comparable to the other samples.All samples were subject to in-silico serotyping using SeqSero (Zhang et al., ) and SISTR (Yoshida et al., ), starting from both raw reads and assembled data, to confirm the in vitro serotyping. […]

library_books

Comprehensive assessment of the quality of Salmonella whole genome sequence data available in public sequence databases using the Salmonella in silico Typing Resource (SISTR)

2018
Microb Genom
PMCID: 5857378
PMID: 29338812
DOI: 10.1099/mgen.0.000151

[…] signed to known STs with an associated serovar. Serovar prediction of an isolate from WGS data using similarity searches of the genes responsible for the serological phenotype has been implemented in SeqSero []. The drawback of using this approach is that multiple serovars can have the same antigenic formula when considered at the serogroup level. Additional complications include that the genetic […]

call_split

Comparative genomics identifies distinct lineages of S. Enteritidis from Queensland, Australia

2018
PLoS One
PMCID: 5770046
PMID: 29338017
DOI: 10.1371/journal.pone.0191042
call_split See protocol

[…] thub.com/tseemann/abricate), and chromosomal point mutations associated with antimicrobial resistance were detected using ResFinder [, ]. The molecular serotype of the QLD isolates was assessed using SeqSero []. […]

library_books

Whole genome sequencing based detection of antimicrobial resistance and virulence in non typhoidal Salmonella enterica isolated from wildlife

2017
PMCID: 5697165
PMID: 29201148
DOI: 10.1186/s13099-017-0213-x

[…] rom reptiles and mammals (Table ). The serovars of 96 isolates in this study were determined at the National Veterinary Service Laboratory, Ames, IA, and the remaining 6 serovars were predicted using Seqsero []. The serovar of one isolate (ADRDL-093) was not identified under Kauffmann-White classification. A total of 45 serovars were identified among the 103 isolates, of which Typhimurium (12.62%) […]

call_split

Draft Genome Sequences of 23 Salmonella enterica Strains Isolated from Cattle in Ibadan, Nigeria, Representing 21 Salmonella Serovars

2017
Genome Announc
PMCID: 5690322
PMID: 29146845
DOI: 10.1128/genomeA.01128-17
call_split See protocol

[…] sing SPAdes version 3.8 (), and genome annotation was performed with the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (). Salmonella serotyping by whole-genome sequencing was predicted with the SeqSero version 1.0 software tool (). The NCBI pathogen detection website (https://www.ncbi.nlm.nih.gov/pathogens) and annotation pipeline () were queried to extract information regarding AMR genes pr […]

Citations

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SeqSero institution(s)
Center for Food Safety, Department of Food Science and Technology, University of Georgia, Griffin, GA, USA; Department of Computer Science, Illinois Institute of Technology, Chicago, IL, USA; Department of Infectious Diseases, J. Craig Venter Institute, Rockville, MD, USA; Department of Biostatistics, School of Public Health, University of Michigan, MI, USA; Biological Sciences Division, Pacific Northwest National Laboratory, Richard, WA, USA; Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
SeqSero funding source(s)
Supported in part by contributions from the Board of Advisors, Center for Food Safety, 420 University of Georgia and University of Georgia startup funds.

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