wavefront-alignment

There are 9 repositories 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:VHDL489311

  • kcleal/pywfa

    Python wrapper for wavefront alignment using WFA2-lib

    Language:Python355132

  • 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:C20202

  • 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:Roff11714

  • 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

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  • urbanslug/wfa

    Rust WFA and WFλ

    Language:Rust7111

  • TWANG006/ortho-poly

    Orthogonal polynomials for optics analysis

    Language:C++4100

  • pityka/pairwisealignment

    pairwise sequence alignment in scala

    Language:Scala3301

  • iFoxz17/WF_Recgraph

    Optimal sequence-to-graph alignment with recombinations using wavefront algorithm.

    Language:Rust0100