SeroBA specifications

Information


Unique identifier OMICS_20599
Name SeroBA
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data Illumina paired-end reads
Input format FASTQ format
Output data The predicted serotype with detailed information, An assembly of the cps locus sequences.
Output format TXT, TSV
Biological technology Illumina
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python, Shell (Bash)
License GNU General Public License version 3.0
Computer skills Advanced
Version 0.1.3
Stability Stable
Maintained Yes

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Documentation


Maintainers


  • person_outline Jacqueline A. Keane <>
  • person_outline Andrew Page <>

Additional information


https://github.com/sanger-pathogens/pathogen-informatics-training

Publication for SeroBA

SeroBA in publication

PMCID: 5728576
PMID: 29236737
DOI: 10.1371/journal.pone.0189163

[…] variations between serotype-specific genes may require regular updating of the pneumocat databases to prevent these misidentifications., another automated serotyping pipeline for s. pneumoniae, seroba, was recently developed and used a hybrid assembly and mapping approach []. although the authors proved that it was faster and less computational-intensive than pneumocat, serotype […]


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SeroBA institution(s)
Pathogen Informatics, Wellcome Trust Sanger Institute, Hinxton, Cambs, UK; Department of Mathematics and Computer Science, Freie Universit├Ąt Berlin, Berlin, Germany; Nuffield Department of Medicine, University of Oxford, Oxford, UK; Infection Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambs, UK

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