stringMLST: a fast k-mer based tool for multilocus sequence typing.
Identifieur interne : 000B08 ( Main/Exploration ); précédent : 000B07; suivant : 000B09stringMLST: a fast k-mer based tool for multilocus sequence typing.
Auteurs : Anuj Gupta [États-Unis] ; I King Jordan [États-Unis] ; Lavanya Rishishwar [États-Unis]Source :
- Bioinformatics (Oxford, England) [ 1367-4811 ] ; 2017.
Descripteurs français
- KwdFr :
- Analyse de séquence d'ADN (), Bactéries (), Bactéries (génétique), Campylobacter jejuni (), Campylobacter jejuni (génétique), Chlamydia trachomatis (), Chlamydia trachomatis (génétique), Logiciel, Neisseria meningitidis (), Neisseria meningitidis (génétique), Streptococcus pneumoniae (), Streptococcus pneumoniae (génétique), Séquençage nucléotidique à haut débit (), Techniques de typage bactérien (), Typage par séquençage multilocus ().
- MESH :
- génétique : Bactéries, Campylobacter jejuni, Chlamydia trachomatis, Neisseria meningitidis, Streptococcus pneumoniae.
- Analyse de séquence d'ADN, Bactéries, Campylobacter jejuni, Chlamydia trachomatis, Logiciel, Neisseria meningitidis, Streptococcus pneumoniae, Séquençage nucléotidique à haut débit, Techniques de typage bactérien, Typage par séquençage multilocus.
English descriptors
- KwdEn :
- Bacteria (classification), Bacteria (genetics), Bacterial Typing Techniques (methods), Campylobacter jejuni (classification), Campylobacter jejuni (genetics), Chlamydia trachomatis (classification), Chlamydia trachomatis (genetics), High-Throughput Nucleotide Sequencing (methods), Multilocus Sequence Typing (methods), Neisseria meningitidis (classification), Neisseria meningitidis (genetics), Sequence Analysis, DNA (methods), Software, Streptococcus pneumoniae (classification), Streptococcus pneumoniae (genetics).
- MESH :
- classification : Bacteria, Campylobacter jejuni, Chlamydia trachomatis, Neisseria meningitidis, Streptococcus pneumoniae.
- genetics : Bacteria, Campylobacter jejuni, Chlamydia trachomatis, Neisseria meningitidis, Streptococcus pneumoniae.
- methods : Bacterial Typing Techniques, High-Throughput Nucleotide Sequencing, Multilocus Sequence Typing, Sequence Analysis, DNA.
- Software.
Abstract
Rapid and accurate identification of the sequence type (ST) of bacterial pathogens is critical for epidemiological surveillance and outbreak control. Cheaper and faster next-generation sequencing (NGS) technologies have taken preference over the traditional method of amplicon sequencing for multilocus sequence typing (MLST). But data generated by NGS platforms necessitate quality control, genome assembly and sequence similarity searching before an isolate's ST can be determined. These are computationally intensive and time consuming steps, which are not ideally suited for real-time molecular epidemiology. Here, we present stringMLST, an assembly- and alignment-free, lightweight, platform-independent program capable of rapidly typing bacterial isolates directly from raw sequence reads. The program implements a simple hash table data structure to find exact matches between short sequence strings (k-mers) and an MLST allele library. We show that stringMLST is more accurate, and order of magnitude faster, than its contemporary genome-based ST detection tools.
DOI: 10.1093/bioinformatics/btw586
PubMed: 27605103
Affiliations:
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Le document en format XML
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Sequencing (methods)</term><term>Multilocus Sequence Typing (methods)</term><term>Neisseria meningitidis (classification)</term><term>Neisseria meningitidis (genetics)</term><term>Sequence Analysis, DNA (methods)</term><term>Software</term><term>Streptococcus pneumoniae (classification)</term><term>Streptococcus pneumoniae (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de séquence d'ADN ()</term><term>Bactéries ()</term><term>Bactéries (génétique)</term><term>Campylobacter jejuni ()</term><term>Campylobacter jejuni (génétique)</term><term>Chlamydia trachomatis ()</term><term>Chlamydia trachomatis (génétique)</term><term>Logiciel</term><term>Neisseria meningitidis ()</term><term>Neisseria meningitidis (génétique)</term><term>Streptococcus pneumoniae ()</term><term>Streptococcus pneumoniae (génétique)</term><term>Séquençage nucléotidique à haut débit ()</term><term>Techniques de typage bactérien ()</term><term>Typage par séquençage multilocus 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We show that stringMLST is more accurate, and order of magnitude faster, than its contemporary genome-based ST detection tools.</div></front></TEI><affiliations><list><country><li>États-Unis</li></country><region><li>Géorgie (États-Unis)</li></region></list><tree><country name="États-Unis"><region name="Géorgie (États-Unis)"><name sortKey="Gupta, Anuj" sort="Gupta, Anuj" uniqKey="Gupta A" first="Anuj" last="Gupta">Anuj Gupta</name></region><name sortKey="Jordan, I King" sort="Jordan, I King" uniqKey="Jordan I" first="I King" last="Jordan">I King Jordan</name><name sortKey="Rishishwar, Lavanya" sort="Rishishwar, Lavanya" uniqKey="Rishishwar L" first="Lavanya" last="Rishishwar">Lavanya Rishishwar</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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