Search Results for "mapper"

Barracuda is a high-speed sequence aligner based on Sanger's BWA and utilizes the latest Nvidia CUDA architecture for accelerating alignments of sequence reads generated by next-generation sequencers.

OLego is a program specifically designed for de novo spliced mapping of mRNA-seq reads. OLego adopts a seeding and extension scheme, and does not rely on a separate external mapper. It achieves high sensitivity of junction detection by using very small seeds (12-14 nt), efficiently mapped using Burrows-Wheeler transform (BWT) and FM-index. This also makes it particularly sensitive for discovering small exons. It is implemented in C++ with full support of multiple threading, to allow fast processing of large-scale data.

SMALT aligns DNA sequencing reads with genomic reference sequences. It employs hashing combined with dynamic programming.

Fast Alignment Search Tool suite. A fast sequence read mapper suite for short reads generated with the Illumina platform. Contains mrFAST and mrsFAST. Joint development by University of Washington and Simon Fraser University

A set of very optimized tools for indexing/querying huge genomes/files. Provided so far: a very fast exact mapper, and an unconstrained split-mapper

BSmapper - Sequence mapper for bisulfite sequencing reads for DNA methylation studies. Can handle Sanger and 454 reads for mapping to whole genomes or target regions.