A versatile pairwise aligner for genomic and spliced nucleotide sequences
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Updated
Jun 18, 2024 - C
A versatile pairwise aligner for genomic and spliced nucleotide sequences
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
Sequence-to-graph mapper and graph generator
Align proteins to genomes with splicing and frameshift
A fast multiple sequence alignment program.
A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment
A reimplementation of the WaveFront Alignment algorithm at low memory
A dotplot generator for large chromosomes
GPU implementation of the Wavefront Alignment Algorithm for global, gap-affine, pairwise sequence alginment
AIM, A Framework for High-throughput Sequence Alignment using Real Processing-in-Memory Systems, Bioinformatics, btad155, https://doi.org/10.1093/bioinformatics/btad155
genomic alignment similarity search tool
Short reads aligner for NIPT/CNV
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…
Fast implementation of Ukkenon's O(ND) algorithm for computing edit distance
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.
A CUDA library of DNA/RNA sequence alignment algorithms.
A parallelized version of multiple DNA sequence alignment algorithm with MPI, OpenMP and CUDA
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)
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