wavefront-alignment
There are 0 repository under wavefront-alignment topic.
CMU-SAFARI / SneakySnake
SneakySnake:snake: is the first and the only pre-alignment filtering algorithm that works efficiently and fast on modern CPU, FPGA, and GPU architectures. It greatly (by more than two orders of magnitude) expedites sequence alignment calculation for both short and long reads. Described in the Bioinformatics (2020) by Alser et al. https://arxiv.org/abs/1910.09020.
Language:VHDL 47- Language:Python 32
safaad / aim
AIM, A Framework for High-throughput Sequence Alignment using Real Processing-in-Memory Systems, Bioinformatics, btad155, https://doi.org/10.1093/bioinformatics/btad155
Language:C 19Genome-on-Diet is a fast and memory-frugal framework for exemplifying sparsified genomics for read mapping, containment search, and metagenomic profiling. It is much faster & more memory-efficient than minimap2 for Illumina, HiFi, and ONT reads. Described by Alser et al. (preliminary version: https://arxiv.org/abs/2211.08157).
Language:Roff 11The first work to provide a comprehensive survey of a prominent set of algorithmic improvement and hardware acceleration efforts for the entire genome analysis pipeline used for the three most prominent sequencing data, short reads (Illumina), ultra-long reads (ONT), and accurate long reads (HiFi). Described in arXiv (2022) by Alser et al. https://arxiv.org/abs/2205.07957
- Language:Rust 7
TWANG006 / ortho-poly
Orthogonal polynomials for optics analysis
Language:C++ 4pityka / pairwisealignment
pairwise sequence alignment in scala
Language:Scala 3iFoxz17 / WF_Recgraph
Optimal sequence-to-graph alignment with recombinations using wavefront algorithm.
Language:Rust 0
