wavefront-alignment
Here are 9 public repositories matching this topic...
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.o…
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Mar 31, 2023 - VHDL
Python wrapper for wavefront alignment using WFA2-lib
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Nov 19, 2024 - Python
AIM, A Framework for High-throughput Sequence Alignment using Real Processing-in-Memory Systems, Bioinformatics, btad155,https://doi.org/10.1093/bioinformatics/btad155
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Apr 12, 2023 - C
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).
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Sep 4, 2024 - Roff
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…
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Jun 14, 2022
Orthogonal polynomials for optics analysis
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Nov 11, 2022 - C++
pairwise sequence alignment in scala
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Jan 25, 2025 - Scala
Optimal sequence-to-graph alignment with recombinations using wavefront algorithm.
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Jul 28, 2023 - Rust
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