Application of two different algorithms for sequence alignment
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Updated
Dec 10, 2017 - C
Application of two different algorithms for sequence alignment
A parallelized version of multiple DNA sequence alignment algorithm with MPI, OpenMP and CUDA
GenStore is the first in-storage processing system designed for genome sequence analysis that greatly reduces both data movement and computational overheads of genome sequence analysis by exploiting low-cost and accurate in-storage filters. Described in the ASPLOS 2022 paper by Mansouri Ghiasi et al. at https://people.inf.ethz.ch/omutlu/pub/GenS…
AlnSeq runs a c coded Smith Waterman, Needleman Wunsch, and an Hirschberg.
A fast multiple sequence alignment program.
This is a fork of PROMALS3D
ALPHAMALIG(ALPHAbet Multiple ALIGnment)
🧬🔍 Smith-Waterman pairwise sequences alignment ✍️🔡
Illumina (and SOLiD) sensitive read mapping tool (cloned from svn:https://scm.gforge.inria.fr/svnroot/storm/, original code from @marta- , with some work done by @yoann-dufresne)
bvSFM (bit-vector sampled FM-index) is a tool for sequence alignment.
A CUDA library of DNA/RNA sequence alignment algorithms.
Parallel sequence alignment program that finds the optimal mutation in one sequence of the other. Parallelizes CPU and GPU using OpenMP and CUDA, and communicates with multiple computers using MPI.
GateSeeder is the first near-memory CPU-FPGA co-design for alleviating both the compute-bound and memory-bound bottlenecks in short and long-read mapping. GateSeeder outperforms Minimap2 by up to 40.3×, 4.8×, and 2.3× when mapping real ONT, HiFi, and Illumina reads, respectively.
🧬 Implementation of the Smith-Waterman algorithm for aligning amino acid sequences.
Fast implementation of Ukkenon's O(ND) algorithm for computing edit distance
AIM, A Framework for High-throughput Sequence Alignment using Real Processing-in-Memory Systems, Bioinformatics, btad155, https://doi.org/10.1093/bioinformatics/btad155
A reimplementation of the WaveFront Alignment algorithm at low memory
GPU implementation of the Wavefront Alignment Algorithm for global, gap-affine, pairwise sequence alginment
Short reads aligner for NIPT/CNV
A dotplot generator for large chromosomes
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