Bonsai: Fast, flexible taxonomic analysis and classification
☆70Apr 9, 2024Updated 2 years ago
Alternatives and similar repositories for bonsai
Users that are interested in bonsai are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Paint genomes with taxa-specific k-mer probabilities☆15Apr 4, 2022Updated 4 years ago
- Genomic neighbor typing of bacterial pathogens using MinHash☆42Jan 10, 2023Updated 3 years ago
- Accurate metagenomic profiling && Fast large-scale sequence/genome searching☆214Apr 24, 2026Updated last week
- C++ tools for NCBI taxonomy tasks☆12Jun 26, 2025Updated 10 months ago
- 🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results☆245Jan 18, 2024Updated 2 years ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Bloocoo is a k-mer spectrum-based read error corrector, designed to correct large datasets with a very low memory footprint.☆12May 22, 2017Updated 8 years ago
- Hidden Markov Model based Copy number caller☆20Dec 9, 2025Updated 4 months ago
- Fast and accurate genomic distances using HyperLogLog☆162Jan 19, 2023Updated 3 years ago
- Remove human reads from a sequencing run☆48Updated this week
- Histosketching Using Little Kmers☆57May 25, 2023Updated 2 years ago
- Strain-level abundances estimation in metagenomic samples using variation graphs☆24Jan 29, 2023Updated 3 years ago
- ProphAsm – a rapid computation of simplitigs directly from k-mer sets☆25Feb 17, 2023Updated 3 years ago
- An efficient index for the colored, compacted, de Bruijn graph☆112Mar 11, 2026Updated last month
- Header-only, gzread-like reader for gzip, bz2, and xz.☆11Aug 8, 2018Updated 7 years ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- de Bruijn graph cOrrectiOn from graph aLignment☆11Jul 20, 2020Updated 5 years ago
- ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refse…☆105Apr 23, 2026Updated last week
- a toolset for fast DNA read set matching and assembly using a new type of reduced kmer☆37Aug 4, 2021Updated 4 years ago
- a toolset for efficient analysis of 10X Genomics linked read data sets, in particular for de novo assembly☆15Nov 27, 2019Updated 6 years ago
- Dashing 2 is a fast toolkit for k-mer and minimizer encoding, sketching, comparison, and indexing.☆71Jun 17, 2024Updated last year
- Lift-over alignments from variant-aware references☆34Mar 4, 2023Updated 3 years ago
- Robust individual and aggregate checksums for nucleotide sequences☆17Mar 3, 2026Updated last month
- Detects human contamination in bam files☆16Sep 10, 2020Updated 5 years ago
- De novo genome assembler.☆11Jul 30, 2018Updated 7 years ago
- Simple, predictable pricing with DigitalOcean hosting • AdAlways know what you'll pay with monthly caps and flat pricing. Enterprise-grade infrastructure trusted by 600k+ customers.
- CAMITAX: Taxon labels for microbial genomes☆31Dec 14, 2023Updated 2 years ago
- Pan-genome inference and genotyping with long noisy or short accurate reads☆120Dec 13, 2024Updated last year
- Accurate and fast taxonomic classification using pseudoaligning☆21Sep 16, 2017Updated 8 years ago
- Refinements of the WFA alignment algorithm with better complexity☆26Mar 31, 2022Updated 4 years ago
- Bacterial Annotation by Learned Representation of Genes☆60Mar 26, 2026Updated last month
- A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences.☆53Updated this week
- Rapid determination of appropriate reference genomes.☆101Jan 22, 2025Updated last year
- a collection of scripts for organising bacterial genomes by species☆81Mar 18, 2022Updated 4 years ago
- Mapping NCBI Genbank accession to GTDB accession☆14Feb 13, 2021Updated 5 years ago
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- Fast and space-efficient taxonomic classification of long reads☆45Aug 25, 2025Updated 8 months ago
- Translocator: local realignment and global remapping enabling accurate translocation detection using single-molecule sequencing long read…☆12Jan 22, 2020Updated 6 years ago
- 1-code framework: docs, C-library, and tools☆26Apr 2, 2026Updated 3 weeks ago
- A genomic minhashing implementation in Rust☆103Jun 17, 2025Updated 10 months ago
- Population-scale detection of non-reference sequence variants using colored de Bruijn Graphs☆26Apr 29, 2024Updated 2 years ago
- Improved structural variant discovery in accurate long reads using sample-specific strings (SFS)☆49Apr 20, 2026Updated last week
- the we-flyin WFA-guided ultralong tiling sequence aligner☆10May 13, 2021Updated 4 years ago