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SRST / Short Read Sequence Typing
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.
stringMLST / string Multi Locus Sequence Typing
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 data structure to find exact matches between short sequence strings (k-mers) and an multi locus sequence typing (MLST) allele library. We show that stringMLST is more accurate, and order of magnitude faster, than its contemporary genome-based sequence type detection tools.
pMLST / plasmid Multilocus Sequence Typing
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.
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 conventional fimH sub-typing, and is suitable for surveillance and outbreak detection. The software enables researchers and primary investigators to rapidly detect the fimH allele in their datasets. It was validated using two different datasets and a subset thereof, covering a total of 32 fimH subtypes.
Multilocus Sequence Typing Easy
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 typing (MLST) profile for each isolate, and predict potentially heterozygous loci. It produces high quality, unambiguous MLST profiles of all 96 isolates, and the sequences of the reference strains are identical to their genotypes. It can detect heterozygous loci in the hybrid strains and identified the sequences of each allele.
ARIBA / Antimicrobial Resistance Identification By Assembly
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. ARIBA reports significantly more details than existing tools, particularly variant calls, enabling a deeper understanding of the resistance associated with each isolate. It generates detailed and customisable output. It supports several public resources, allowing the user to download the data easily and convert it into a form for use with the pipeline.
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