CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows–Wheeler transform

Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming

(2011) Jochen Blom et al.   BIOINFORMATICS

DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI

(2011) Yongchao Liu et al.   BMC BIOINFORMATICS

GPU-BLAST: using graphics processors to accelerate protein sequence alignment

(2010) P. D. Vouzis et al.   BIOINFORMATICS

CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments

(2010) Lakshmi Kuttippurathu et al.   BIOINFORMATICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

PASS: a program to align short sequences

(2009) D. Campagna et al.   BIOINFORMATICS

SOAP2: an improved ultrafast tool for short read alignment

(2009) R. Li et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

CUDA–MEME: Accelerating motif discovery in biological sequences using CUDA-enabled graphics processing units

(2009) Yongchao Liu et al.   PATTERN RECOGNITION LETTERS

BFAST: An Alignment Tool for Large Scale Genome Resequencing

(2009) Nils Homer et al.   PLoS One

SHRiMP: Accurate Mapping of Short Color-space Reads

(2009) Stephen M. Rumble et al.   PLoS Computational Biology

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Compressed indexing and local alignment of DNA

(2008) T. W. Lam et al.   BIOINFORMATICS

SOAP: short oligonucleotide alignment program

(2008) R. Li et al.   BIOINFORMATICS

Using quality scores and longer reads improves accuracy of Solexa read mapping

(2008) Andrew D Smith et al.   BMC BIOINFORMATICS

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH

NVIDIA Tesla: A Unified Graphics and Computing Architecture

(2008) Erik Lindholm et al.   IEEE MICRO