Fast and accurate de novo assembler for long reads
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Updated
May 10, 2024 - C
Fast and accurate de novo assembler for long reads
abPOA: an SIMD-based C library for fast partial order alignment using adaptive band
TideHunter: efficient and sensitive tandem repeat detection from noisy long reads using seed-and-chain
TideHunter: efficient and sensitive tandem repeat detection from noisy long reads using seed-and-chain
abPOA: an SIMD-based C library for fast partial order alignment using adaptive band
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…
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.
SMIS: Single Molecular Integrative Scaffolding. A pipeline for scaffolding genome assemblies using long reads (PacBio, ONT)
TideHunter: efficient and sensitive tandem repeat detection from noisy long reads using seed-and-chain
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