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pre-alignment-filtering

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CMU-SAFARI / SneakySnake

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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…

fpga gpu smith-waterman needleman-wunsch sequence-alignment long-reads minimap2 short-reads hardware-accelerator sequence-aligner edlib pre-alignment-filtering wavefront-alignment
  • Updated Mar 31, 2023
  • VHDL

CMU-SAFARI / GenASM

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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-analys…

approximate-string-matching read-mapping hw-sw-co-design read-alignment bitap-algorithm pre-alignment-filtering genome-sequence-analysis
  • Updated Dec 19, 2022
  • C

CMU-SAFARI / GenStore

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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/GenS…

ftl ssd sequence-alignment read-mapping long-reads hardware-accelerator near-data-processing pre-alignment-filtering in-storage-processing exact-matching
  • Updated Apr 6, 2022
  • C

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