BIOINFORMATICS

BARRACUDA

Started in 2009, the aim of the BarraCUDA project is to develop a sequence mapping software that utilizes the massive parallelism of graphics processing units (GPUs) to accelerate the inexact alignment of short sequence reads to a particular location on a reference genome.

CUDASW++

CUDASW++ software is a public open source software for Smith-Waterman protein database searches on Graphics Processing Units (GPUs) with CUDA.

GATK

GATK is the industry standard for identifying SNPs and indels in germline DNA and RNAseq data. Its scope is now expanding to include somatic variant calling tools, and to tackle copy number (CNV) and structural variation (SV). In addition to the variant callers themselves, the GATK also includes many utilities to perform related tasks such as processing and quality control of high-throughput sequencing data.

G-BLASTN

G-BLASTN is a GPU-accelerated nucleotide alignment tool based on the widely used NCBI-BLAST. G-BLASTN supports the blastn and megablast modes of NCBI-BLAST, and can produce exactly the same results as NCBI-BLAST.

GPU-BLAST

The Basic Local Alignment Search Tool (BLAST) is one of the most widely used bioinformatics tools. The widespread impact of BLAST is reflected in over 110,000 citations that this software has received in the past three decades, and the use of the word “blast” as a verb referring to biological sequence comparison. Any improvement in the execution speed of BLAST would be of great importance in the practice of bioinformatics, and facilitate coping with ever increasing sizes of biomolecular databases.

MCUDA-MEME

mCUDA-MEME is an ultrafast scalable motif discovery algorithm based on MEME algorithm for multiple GPUs using a hybrid combination of CUDA, MPI and OpenMP parallel programming models.

SEQNFIND

The SeqNFind is a powerful tool suite that addresses the need for complete and accurate alignments of many small sequences against entire genomes utilizing a unique hardware/software cluster system that leverages a multi-processing GPU environment to do fast and complete short read genomic sequence alignments. SeqNFind utilizes a database linked cross-platform, Graphical User Interface (GUI) based toolset for facilitating bioinformatics research.

SOAP3

SOAP3 is a GPU-based software for aligning short reads with a reference sequence. It can find all alignments with k mismatches, where k is chosen from 0 to 3.

SOAP3-DP

SOAP3-dp like its predecessor SOAP3, is a GPU-based software for aligning short reads to a reference sequence. It improves SOAP3 regarding both speed and sensitivity by skillful exploitation of whole-genome indexing and dynamic programming on a GPU. SOAP3 is limited to find alignments with at most four mismatches, while SOAP3-dp can find alignments involving mismatches, INDELs, and small gaps. The number of reads aligned, especially for paired-end data, typically increases 5 to 10 percent from SOAP3 to SOAP3-dp. More interestingly, SOAP3-dp’s alignment time is much shorter than SOAP3, as it is found that GPU-based dynamic programming, when coupled with indexing, can be much more efficient. For example, when aligning length-100 single-end reads with the human genome, SOAP3 typically requires tens of seconds per million reads, while SOAP3-dp takes only a few seconds.