GitHub topics: wavefront-alignment
pityka/pairwisealignment
pairwise sequence alignment in scala
Language: Scala - Size: 52.7 KB - Last synced at: about 1 month ago - Pushed at: 3 months ago - Stars: 3 - Forks: 1
kcleal/pywfa
Python wrapper for wavefront alignment using WFA2-lib
Language: Python - Size: 690 KB - Last synced at: 5 days ago - Pushed at: 6 months ago - Stars: 35 - Forks: 3
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 - Size: 21.2 MB - Last synced at: 6 months ago - Pushed at: about 2 years ago - Stars: 48 - Forks: 11
CMU-SAFARI/Genome-on-Diet
Genome-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 - Size: 63 MB - Last synced at: 9 months ago - Pushed at: over 1 year ago - Stars: 11 - Forks: 4
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 - Size: 1.18 MB - Last synced at: about 1 year ago - Pushed at: about 2 years ago - Stars: 19 - Forks: 2
CMU-SAFARI/Molecules2Variations
The 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
Size: 4.31 MB - Last synced at: 9 months ago - Pushed at: almost 3 years ago - Stars: 8 - Forks: 0
iFoxz17/WF_Recgraph
Optimal sequence-to-graph alignment with recombinations using wavefront algorithm.
Language: Rust - Size: 15.5 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 1 - Forks: 0
urbanslug/wfa
Rust WFA and WFλ
Language: Rust - Size: 752 KB - Last synced at: over 1 year ago - Pushed at: about 3 years ago - Stars: 7 - Forks: 1
TWANG006/ortho-poly
Orthogonal polynomials for optics analysis
Language: C++ - Size: 7.05 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 4 - Forks: 0
