Multilocus sequence typing software tools | Whole-genome sequencing data 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 alternative to some traditional typing methods for public health infectious disease surveillance.
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 users to determine bonds between the predicted founding genotype and the other genotypes in the group. It also includes functions for comparing two datasets for highlight existing sequence type (STs) and detect similarities.
Provides various next-generation sequencing (NGS) data analysis applications which are developed or optimized by Illumina, or from a growing ecosystem of third-party app providers. BAseSpace is a cloud platform that can be integrated with the industry’s leading sequencing platforms, without cumbersome or time consuming data transfer steps.
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 bacterial genomic sequence data, which offers several advantages over traditional multi-locus sequence typing (MLST). SRST is designed to perform two key tasks: detect the presence of a gene or locus and determine the precise or closest matching allele for that locus, among a set of possible reference allele sequences.
It is designed for distributed work-groups (client/server model) and allows automatic processing and analyzing of NGS (e.g., Illumina, Ion Torrent or PacBio) and Sanger capillary-electrophoresis sequence data. SeqSphere+ is the solution for easy and automated microbial analysis; enabling your lab to employ whole genome microbial typing (MLST+), traditional MLST or eMLST/rMLST sequencing projects. With fast and affordable microbial whole genome shotgun (WGS) next generation sequencing and automatized software analysis, microbiologists can use genome-wide hundreds/thousands of genes (core genome MLST or MLST+) for typing, resulting in higher discrimination and more accurate strain typing. The heightened discrimination power of MLST+, coupled with rapid and simple workflow NGS, makes this complete solution ideal for everyday microbial monitoring to outbreak investigation.
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 same variety of data for the five incompatibility groups that currently have a pMLST scheme available. The software uses the BLASTn algorithm for finding DNA homologies in both raw and assembled sequences. It is able to isolate and subtype IncHI1, IncHI2, IncI1, and IncF plasmids present among the isolates.
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 of the O-antigen processing genes and the flagellin genes. For some isolates, SerotypeFinder can detect more than one flagellin gene. This application is an advantageous alternative to the current routine.
Offers a platform dedicated to investigation related to methicillin-resistant Staphylococcus aureus bacteria (MRSA). StaphType is a program intending to assist users in typing MRSA by identifying and gathering information linked with their spa repeats and spa-types. It includes a repeat motif search, a report generator and a feature to locally host information from previous analysis.