Ecosyste.ms: Repos
An open API service providing repository metadata for many open source software ecosystems.
GitHub topics: pre-alignment-filtering
CMU-SAFARI/GenASM
Source code for the software implementations of the GenASM algorithms proposed in our MICRO 2020 paper: Senol Cali et. al., "GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis" at https://people.inf.ethz.ch/omutlu/pub/GenASM-approximate-string-matching-framework-for-genome-analysis_micro20.pdf
Language: C - Size: 44.9 KB - Last synced: about 1 month ago - Pushed: over 1 year ago - Stars: 29 - Forks: 7
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: about 1 month ago - Pushed: about 1 year ago - Stars: 46 - Forks: 10
CMU-SAFARI/GenStore
GenStore is the first in-storage processing system designed for genome sequence analysis that greatly reduces both data movement and computational overheads of genome sequence analysis by exploiting low-cost and accurate in-storage filters. Described in the ASPLOS 2022 paper by Mansouri Ghiasi et al. at https://people.inf.ethz.ch/omutlu/pub/GenStore_asplos22-arxiv.pdf
Language: C - Size: 2.26 MB - Last synced: about 1 month ago - Pushed: about 2 years ago - Stars: 12 - Forks: 0