SRST 2-0.2.0 – Short Read Sequence Typing for Bacterial Pathogens

SRST 2-0.2.0

:: DESCRIPTION

SRST is designed to take Illumina sequence data, a MLST database and/or a database of gene sequences (e.g. resistance genes, virulence genes, etc) and report the presence of STs and/or reference genes.

::DEVELOPER

Bernie Pope

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ Windows/MacOsX
Python
bowtie2
SAMtools

:: DOWNLOAD

SRST

:: MORE INFORMATION

Citation

Genome Med. 2014 Nov 20;6(11):90. doi: 10.1186/s13073-014-0090-6. eCollection 2014.
SRST2: Rapid genomic surveillance for public health and hospital microbiology labs.
Inouye M, Dashnow H, Raven LA, Schultz MB, Pope BJ, Tomita T, Zobel J, Holt KE

BMC Genomics. 2012 Jul 24;13:338.
Short read sequence typing (SRST): multi-locus sequence types from short reads.
Inouye M, Conway TC, Zobel J, Holt KE.

RV-Typer – Typing of Rhinoviruses Using Alignment-Free Approach

RV-Typer

:: DESCRIPTION

RV-Typer server assigns serotype to Rhinovirus -A, -B & -C using geomic/protein sequences.

::DEVELOPER

Bioinformatics Centre, Savitribai Phule Pune University (formerly University of Pune),

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation:

RV-Typer: A Web Server for Typing of Rhinoviruses Using Alignment-Free Approach.
Kolekar PS, Waman VP, Kale MM, Kulkarni-Kale U.
PLoS One. 2016 Feb 12;11(2):e0149350. doi: 10.1371/journal.pone.0149350.

PHYLOViZ 1.0 – Phylogenetic Inference and Data Visualization for Sequence based Typing Methods

PHYLOViZ 1.0

:: DESCRIPTION

Phyloviz is platform independent JAVA software that allows the analysis of sequence-based typing methods that generate allelic profiles and their associated epidemiological data.

::DEVELOPER

PHYLOViZ team

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Windows/ MacOsX
Java

:: DOWNLOAD

PHYLOViZ

:: MORE INFORMATION

Citation

PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods.
Francisco AP, Vaz C, Monteiro PT, Melo-Cristino J, Ramirez M, Carri?o JA.
BMC Bioinformatics. 2012 May 8;13:87. doi: 10.1186/1471-2105-13-87.