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Multilocus sequence typing software tools | Whole-genome sequencing analysis

The process of whole genome sequencing (WGS) has benefited from recent advances collectively known as next generation sequencing, allowing high throughput sequencing of bacterial genomes at low financial cost. This results in WGS becoming a viable…
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MetaMLST
Desktop

MetaMLST Meta Multi Locus Sequence Typing

Allows to work about microbial typing. MetaMLST performs an in-silico consensus…

Allows to work about microbial typing. MetaMLST performs an in-silico consensus sequence reconstruction of the allelic profile of the microbial strains in a metagenomics sample. It identifies the…

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stringMLST
Desktop

stringMLST string Multi Locus Sequence Typing

An assembly- and alignment-free, lightweight, platform-independent program…

An assembly- and alignment-free, lightweight, platform-independent program capable of rapidly typing bacterial isolates directly from raw sequence reads. stringMLST implements a simple hash table…

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SerotypeFinder
Web

SerotypeFinder

Enables rapid and accurate WGS-based routine (O:H) serotyping of Escherichia…

Enables rapid and accurate WGS-based routine (O:H) serotyping of Escherichia coli. SerotypeFinder is a publicly available Center for Genomic Epidemiology (CGE) web tool. It was developed on the basis…

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pMLST
Web

pMLST plasmid Multilocus Sequence Typing

Allows analysis and classification of plasmids from bacterial species of the…

Allows analysis and classification of plasmids from bacterial species of the family Enterobacteriaceae. pMLST is a web server that performs plasmid Multilocus Sequence Typing (pMLST) analysis on the…

LOCUST
Desktop
Web

LOCUST LOcus CUstom Sequence Typer

Allows users to customize the typing of microbial isolates from whole genome…

Allows users to customize the typing of microbial isolates from whole genome sequencing (WGS) data. LOCUST can generate a seed file from a given set of alleles. It is able to type bacterial genomes…

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ARIBA
Desktop

ARIBA Antimicrobial Resistance Identification By Assembly

Uses a combined mapping/alignment and targeted local assembly approach to…

Uses a combined mapping/alignment and targeted local assembly approach to identify antimicrobial resistance (AMR) genes and variants efficiently and accurately from Illumina paired sequencing reads.…

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SRST
Desktop

SRST Short Read Sequence Typing

A software for quick and accurate retrieval of sequence types from short read…

A software for quick and accurate retrieval of sequence types from short read sets, using inputs easily downloaded from public databases. SRST uses read mapping to assign sequence types to novel…

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FimTyper
Web

FimTyper

Identifies fimH alleles from either simple Sanger generated sequences, as well…

Identifies fimH alleles from either simple Sanger generated sequences, as well as raw or assembled whole genome sequencing (WGS) data from E. coli genomes. FimTyper consists in an alternative to…

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Multilocus…
Desktop

Multilocus Sequence Typing Easy

Represents a program for data analyses. MLSTEZ enables to identify the barcodes…

Represents a program for data analyses. MLSTEZ enables to identify the barcodes and primers used in the polymerase chain reaction (PCR), correct sequencing errors, generate the multilocus sequence…

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GrapeTree
Desktop

GrapeTree

Provides a graphical visualization of relationships between large datasets of…

Provides a graphical visualization of relationships between large datasets of phylogenetic trees related to bacterial pathogens. GrapeTree is software that can be available both as a part of the…

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BTyper
Desktop

BTyper

Provides a method for virulence-based classification of Bacillus cereus group…

Provides a method for virulence-based classification of Bacillus cereus group isolates and/or antimicrobial resistance gene detection using nucleotide sequencing data. BTyper is a computational tool…

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SeroBA
Desktop

SeroBA

Enables to detect serotypes from S. pneumoniae Illumina Next Generation…

Enables to detect serotypes from S. pneumoniae Illumina Next Generation Sequencing (NGS) reads using a k-mer based method. SeroBA can provide the Capsular Polysaccharide Biosynthesis (CPS) locus at…

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MentaLiST
Desktop

MentaLiST

Handles large Multi-Locus Sequence Typing (MLST) schemes. MentaLiST can call…

Handles large Multi-Locus Sequence Typing (MLST) schemes. MentaLiST can call the alleles for any given sample, by counting k-mers assigned to each allele, filtering out reads that do not reach a…

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MOST
Desktop

MOST Metric Oriented Sequence Typer

A modified MultiLocus Sequence Typing (MLST) typing tool. MOST is an effective…

A modified MultiLocus Sequence Typing (MLST) typing tool. MOST is an effective method, based on short read sequence data derived from Whole Genome Sequencing (WGS), to describe bacterial populations.…

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StrainSeeker
Desktop

StrainSeeker

Constructs a list of specific k-mers for each node of any given Newick-format…

Constructs a list of specific k-mers for each node of any given Newick-format tree and enables rapid identification of bacterial genomes. StrainSeeker can identify bacterial strains from highly…

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BURST
Web
Desktop

BURST

Aims to determine the founding genotype of a group. BURST is a software…

Aims to determine the founding genotype of a group. BURST is a software available both as a web application and as a standalone software. The program is based on a graphic matroid approach and allows…

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PAst
Web

PAst Pseudomonas aeruginosa serotyper

Provides in silico serotyping of Pseudomonas aeruginosa isolates into 1 of 11…

Provides in silico serotyping of Pseudomonas aeruginosa isolates into 1 of 11 serogroups (covering the 20 serotypes). PAst is a program that runs on next generation sequencing data and is based on a…

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SpaServer…
Dataset

SpaServer Database

Collates and harmonizes data from various geographic regions. SpaServer is a…

Collates and harmonizes data from various geographic regions. SpaServer is a database of Staphylococcus aureus, a major human pathogen causing skin and tissue infections, pneumonia, septicemia, and…

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spaTyper
Web

spaTyper

Predicts the Staphylococcus aureus spa type. spaTyper is a web app that allows…

Predicts the Staphylococcus aureus spa type. spaTyper is a web app that allows users to upload their own data.

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