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CMU-SAFARI / GenASM

Star 30

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
RawHash

CMU-SAFARI / RawHash

Star 39

RawHash is the first mechanism that can accurately and efficiently map raw nanopore signals to large reference genomes (e.g., a human reference genome) in real-time without using powerful computational resources (e.g., GPUs). Described by Firtina et al. (published at https://academic.oup.com/bioinformatics/article/39/Supplement_1/i297/7210440)

bioinformatics nanopore seeding segmentation event-detection genome-analysis hash-tables contamination read-mapping relative-abundances nanopore-sequencing nanopore-analysis-pipeline nanopore-reads nanopore-data nanopore-minion raw-signal rawhash raw-nanopore-signal-analysis
  • Updated Jun 17, 2024
  • C

CMU-SAFARI / BLEND

Star 34

BLEND is a mechanism that can efficiently find fuzzy seed matches between sequences to significantly improve the performance and accuracy while reducing the memory space usage of two important applications: 1) finding overlapping reads and 2) read mapping. Described by Firtina et al. (published in NARGAB https://doi.org/10.1093/nargab/lqad004)

bioinformatics genome-analysis genome-assembly blend read-mapping de-novo-assembly minimizers strobemers seed-matching fuzzy-seeds read-overlapping spaced-seeds
  • Updated May 10, 2023
  • C

CMU-SAFARI / GenStore

Star 12

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

CMU-SAFARI / GateSeeder

Star 7

GateSeeder is the first near-memory CPU-FPGA co-design for alleviating both the compute-bound and memory-bound bottlenecks in short and long-read mapping. GateSeeder outperforms Minimap2 by up to 40.3×, 4.8×, and 2.3× when mapping real ONT, HiFi, and Illumina reads, respectively.

bioinformatics fpga genomics indexing seeding hbm sequence-alignment read-mapping long-reads minimap2 minimizers short-reads genome-on-diet
  • Updated Oct 3, 2023
  • C

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