Approximate nearest neighbour search for microbial genomes based on hash metric
☆61Dec 14, 2025Updated 2 months ago
Alternatives and similar repositories for gsearch
Users that are interested in gsearch are comparing it to the libraries listed below
Sorting:
- Minimum plain text representation of kmer sets☆16Jan 30, 2025Updated last year
- Embedding-based indexing for compact storage and rapid querying of bacterial pan-genomes☆21Dec 9, 2025Updated 3 months ago
- FMSI is a highly memory efficient exact k-mer set index based on masked superstrings and the masked Burrows-Wheeler transform☆24Nov 20, 2025Updated 3 months ago
- Iterate over minimizers of a DNA sequence☆31Jul 12, 2024Updated last year
- A SIMD-accelerated library to compute random minimizers☆39Mar 1, 2026Updated last week
- Fast and Memory Efficient Genome Sketching via HyperLogLog, HyperMinHash and UltraLogLog☆19Jan 22, 2026Updated last month
- Taxonomy classification of viral sequences / contigs☆12Jul 15, 2025Updated 7 months ago
- Development repo for pyani-plus (the next iteration of pyani)☆25Updated this week
- Genomic neighbor typing of bacterial pathogens using MinHash☆42Jan 10, 2023Updated 3 years ago
- Split k-mer analysis – version 2☆104Jan 29, 2026Updated last month
- Space-efficient pseudoalignment with a colored de Bruijn graph☆52Mar 13, 2025Updated 11 months ago
- Index kmtricks bf matrices☆46Feb 13, 2026Updated 3 weeks ago
- MetagenOmic read Re-Assigner and abundance quantifier☆20Jan 31, 2025Updated last year
- genome_updater is a bash script that downloads and updates (non-redundant) snapshots of the NCBI Genomes repository (RefSeq/GenBank) with…☆167Feb 11, 2026Updated 3 weeks ago
- Follow up to Grace Blackwell's 661k dataset, for 2023☆135Feb 26, 2026Updated last week
- MetaProFi is a bloom filter based tool for storing and querying sequence data for accurate identification of functionally relevant geneti…☆12Apr 14, 2022Updated 3 years ago
- PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)☆104Feb 9, 2026Updated last month
- RabbitTClust: enabling fast clustering analysis of millions bacteria genomes with MinHash sketches☆53Updated this week
- Generate kmers/minimizers/hashes/MinHash signatures, including with multiple kmer sizes.☆24Jan 9, 2021Updated 5 years ago
- kaamer - protein identification based on amino acid kmers☆12Mar 7, 2023Updated 3 years ago
- Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.☆236Oct 12, 2025Updated 4 months ago
- Fast and space-efficient taxonomic classification of long reads☆45Aug 25, 2025Updated 6 months ago
- fast, multithreaded sourmash operations: search, compare, and gather.☆25Updated this week
- ViromeScan allows the user to explore and taxonomically characterize the virome from metagenomic reads, efficiently denoising samples fro…☆13Feb 13, 2023Updated 3 years ago
- ☆16Jan 21, 2024Updated 2 years ago
- Rust bindings to minimap2 library☆109Mar 2, 2026Updated last week
- Aligns short reads using dynamic seed size with strobemers☆192Updated this week
- ProphAsm – a rapid computation of simplitigs directly from k-mer sets☆25Feb 17, 2023Updated 3 years ago
- Interactive, web tool for exploring pan-genome of bacterial strains☆49Jan 14, 2026Updated last month
- Contains the description of a file format to store kmers and associated values☆34Aug 17, 2022Updated 3 years ago
- COBS - Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams)☆20Nov 24, 2024Updated last year
- A small, auxiliary index to massively improve parallel fastq parsing☆31Updated this week
- Mandrake 🌿/👨🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding☆39Mar 7, 2025Updated last year
- LexicMap: efficient sequence alignment against millions of prokaryotic genomes☆214Feb 28, 2026Updated last week
- Taxonomic classifier for sequencing reads (bulk and single-cell data, short and long read) using FM-index with run-block compressed BWT.☆87Feb 18, 2026Updated 2 weeks ago
- Bifrost graph gene caller.☆98Jan 20, 2026Updated last month
- Needleman-Wunsch Alignment in Go☆12Nov 9, 2020Updated 5 years ago
- HyGen: Compact and Efficient Genome Sketching using Hyperdimensional Vectors☆30Aug 26, 2024Updated last year
- A curated database of completed assemblies with taxonomy IDs☆51Feb 25, 2026Updated last week