PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.
☆29Aug 20, 2025Updated 6 months ago
Alternatives and similar repositories for pyskani
Users that are interested in pyskani are comparing it to the libraries listed below
Sorting:
- A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.☆35Jul 21, 2025Updated 7 months ago
- PyO3 bindings and Python interface to sylph, an ultrafast method for containment ANI querying and taxonomic profiling.☆20Dec 12, 2024Updated last year
- Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.☆236Oct 12, 2025Updated 4 months ago
- Efficient and fast querying and parsing of GTDB's data☆29Aug 21, 2025Updated 6 months ago
- Cython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation.☆24Oct 15, 2025Updated 4 months ago
- Follow up to Grace Blackwell's 661k dataset, for 2023☆135Feb 26, 2026Updated last week
- ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.☆297Feb 3, 2026Updated last month
- Overview of our data for microbial genomic benchmarking☆35Feb 5, 2026Updated last month
- RabbitTClust: enabling fast clustering analysis of millions bacteria genomes with MinHash sketches☆53Feb 28, 2026Updated last week
- Genome size estimation from long read overlaps☆81Updated this week
- Rapid & standardized annotation of bacterial genomes, MAGs & plasmids using protein structural information☆42Feb 25, 2026Updated last week
- A repo with just adapter sequences☆15Jul 7, 2025Updated 7 months ago
- Split k-mer analysis – version 2☆104Jan 29, 2026Updated last month
- Compute a pairwise SNP distance matrix from one or two alignment(s)☆26Sep 12, 2024Updated last year
- Bioinformatics tool for Locus Visualisation☆160Updated this week
- µbinfie blog☆19Jul 21, 2025Updated 7 months ago
- Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)☆41Apr 17, 2024Updated last year
- Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!☆178Jan 7, 2026Updated last month
- Binning Virus Genomes from Metagenomes☆72Jul 13, 2022Updated 3 years ago
- Chimera: A Versatile Metagenomic Classification Tool☆20Feb 1, 2026Updated last month
- ☆26Feb 28, 2026Updated last week
- Microbial agile accurate SNP Typer☆30Dec 27, 2023Updated 2 years ago
- Circular bacterial genome plots based on BLAST or NUCMER/PROMER alignments☆108Dec 11, 2023Updated 2 years ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆65Apr 10, 2025Updated 10 months ago
- Bifrost graph gene caller.☆98Jan 20, 2026Updated last month
- Standalone Python re-implementation of the POLCA polisher from MaSuRCA☆44Aug 20, 2025Updated 6 months ago
- geNomad: Identification of mobile genetic elements☆291Nov 10, 2025Updated 3 months ago
- A Pyrodigal extension to predict genes in giant viruses and viruses with alternative genetic code.☆22Nov 25, 2025Updated 3 months ago
- Fast and space-efficient taxonomic classification of long reads☆45Aug 25, 2025Updated 6 months ago
- LexicMap: efficient sequence alignment against millions of prokaryotic genomes☆214Updated this week
- Map query sequences to the assemblies of all pre-June 2023 bacteria (https://ftp.ebi.ac.uk/pub/databases/AllTheBacteria/Releases/0.2/) on…☆12May 22, 2024Updated last year
- Rust coder/decoder for Nucleotide Archival Format (NAF) files.☆10Jan 31, 2025Updated last year
- ☆10Jun 9, 2025Updated 8 months ago
- Drug Resistance Prediction with Reference Graphs☆21Oct 23, 2025Updated 4 months ago
- alignment-free coverage calculation for metagenomic binning >100 times faster☆50Mar 13, 2025Updated 11 months ago
- A versatile toolkit for k-mers with taxonomic information☆82Aug 28, 2025Updated 6 months ago
- Aligns short reads using dynamic seed size with strobemers☆192Feb 27, 2026Updated last week
- A Python package for obtaining, parsing and exploring biological taxonomies (GTDB, NCBI, Silva, Greengenes, OTT)☆47Feb 5, 2026Updated last month
- Remove human reads from a sequencing run☆48Updated this week