||the first distribution of the CUSHAW software package for NGS read alignment. It is a CUDA compatible short read alignment algorithm for multiple GPUs sharing a single host. This aligner only provides support for ungapped alignment and has been incorporated to NVIDIA Tesla Bio Workbench.
||the second distribution of the CUSHAW software package for NGS read alignment. It is a fast and parallel gapped read alignment to large genomes, such as the human genome. This aligner has been further accelerated using GPU computing and is implemented in CUSHAW2-GPU.
||the third distribution of the CUSHAW software package for NGS read alignment. It is a parallel, sensitive and accurate short-read aligner for both base-space and color-space single-end/paired-end reads. This aligners has been further enhanced using cluster computing and is implemented in CUSHAW3-UPC.
|Short-read error correction
||the first parallel and distributed pre-assembly short read error correction algorithm using CUDA and MPI.
||a parallel and scalable multistage k-mer spectrum based error corrector for Illumina sequence data.
||a parallel multistage homopolymer spectrum based error corrector to handle homopolymer insertions or deletions in 454 sequencing data.
||a parallelized short read assembler for large genomes, such as the human genome, using de Bruijn graphs.
||an integrated caller for germline and somatic single nucleotide variants (SNVs) in diploid genomes.
||a software pipeline for quantitative measurement of species composition in foodstuff material.
|Pairwise sequence alignment
||the fastest parallel Smith Waterman protein database search algorithm for GPGPUs using CUDA.
||the first parallel algorithm to accelerate the Smith-Waterman protein database search on Xeon Phi coprocessors.
||the first parallel Smith-Waterman algorithm exploiting Xeon Phi clusters to accelerate the alignment of long DNA sequences.
||a Bit-parallel approximate pattern matching algorithm that is based on the Wu-Manber algorithm and further accelerated by Xeon Phi coprocessors.
|Multiple sequence alignment
|| a well-established state-of-the-art multiple sequence alignment algorithm for protein sequences, which produces the highest alignment accuracy compared to the existing leading aligners.