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strobemers

Here are 6 public repositories matching this topic...

ksahlin / strobealign

Aligns short reads using dynamic seed size with strobemers

bioinformatics alignment illumina short-read-mapping strobemers

Updated Oct 23, 2024
C++

ksahlin / ultra

Long-read splice alignment with high accuracy

bioinformatics alignment long-read-sequencing strobemers

Updated Sep 26, 2024
Python

CMU-SAFARI / BLEND

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

shenwei356 / strobemers

A Go implementation of the strobemers (https://github.com/ksahlin/strobemers)

Updated Apr 23, 2021
Go

luispedro / strobefilter

Benchmarking pre-filtering large databases before short-read mapping

bioinformatics metagenomics strobemers

Updated Aug 9, 2024
Python

imzoc / fast-similarity-methods-rust

Rust implementation of alignment-free similarity estimation methods.

bioinformatics minhash strobemers sequence-sketching

Updated Aug 25, 2024
Rust

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