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Sneakysnake ⭐ 44

SneakySnake🐍 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.

SIMD C/C++ library for massive optimal sequence alignment (local/SW, infix, overlap, global)

Seqalign ⭐ 14

Collection of sequence alignment algorithms.

Cython bindings and Python interface to Opal, a SIMD-accelerated database search aligner.

GPU-based DNA sequence alignment program using Smith-Waterman

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