HyGen: Compact and Efficient Genome Sketching using Hyperdimensional Vectors
☆33Aug 26, 2024Updated last year
Alternatives and similar repositories for Hyper-Gen
Users that are interested in Hyper-Gen are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Python and Rust library for loading, saving, and manipulating taxonomic trees☆54Jun 22, 2026Updated last month
- A Python package for obtaining, parsing and exploring biological taxonomies (GTDB, NCBI, Silva, Greengenes, OTT)☆51May 5, 2026Updated 2 months ago
- Taxonomy classification of viral sequences / contigs☆12Jul 15, 2025Updated last year
- Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]☆48Jun 19, 2026Updated last month
- process any file in tabular format. Fasta/fastq/GTF/GFF/VCF/SAM/BED☆24Aug 22, 2025Updated 11 months ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- MetaProFi is a bloom filter based tool for storing and querying sequence data for accurate identification of functionally relevant geneti…☆13Apr 14, 2022Updated 4 years ago
- Contains the code and workflow for the bacterial strain definition paper with Kostas Kostantinidis☆14Dec 4, 2023Updated 2 years ago
- PanTax: Strain-level metagenomic profiling using pangenome graphs☆55Jun 10, 2026Updated last month
- kmer based feature extraction tool for bioinformatics, metagenomics, AI/ML and more☆47Jul 12, 2026Updated last week
- RabbitMash: an efficient highly optimized implementation of Mash.☆20Oct 28, 2023Updated 2 years ago
- k-mers and the like☆23Updated this week
- MAGScoT - a MAG scoring and refinement tool☆48Apr 8, 2026Updated 3 months ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆69Apr 10, 2025Updated last year
- Fast sequence distance estimates☆30Jul 1, 2026Updated 3 weeks ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- ☆20Jan 13, 2026Updated 6 months ago
- Minimum plain text representation of kmer sets☆18Jan 30, 2025Updated last year
- Fasten toolkit, for streaming operations on fastq files☆82Oct 24, 2025Updated 9 months ago
- Chimera: A Versatile Metagenomic Classification Tool☆21Jul 17, 2026Updated last week
- Leviathan: A fast, memory-efficient, and scalable taxonomic and pathway profiler for (pan)genome-resolved metagenomics and metatranscript…☆26Updated this week
- Host depletion optimised for clinical metagenomic sequencing applications☆19Jul 9, 2026Updated 2 weeks ago
- Fast and Memory Efficient Genome Sketching via HyperLogLog, HyperMinHash and UltraLogLog☆22Jan 22, 2026Updated 6 months ago
- Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.☆259May 13, 2026Updated 2 months ago
- Compacted and colored de Bruijn graph construction and querying☆98Jul 1, 2026Updated 3 weeks ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- A versatile toolkit for k-mers with taxonomic information☆84Aug 28, 2025Updated 10 months ago
- A functional profiler for metagenomes using FracMinHash☆21Apr 20, 2026Updated 3 months ago
- Hierarchical binned indexed data store for on-disk genomic data.☆13Jan 18, 2025Updated last year
- A high-performance in-silico PCR tool for primer matching and product extraction from FASTA and GenBank sequences.☆18Feb 25, 2026Updated 4 months ago
- Extremely fast and accurate Nanopore demultiplexing☆101Updated this week
- ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.☆314Feb 3, 2026Updated 5 months ago
- An R package for learning log-ratio biomarkers from high-throughput sequencing data.☆23Mar 31, 2023Updated 3 years ago
- An extensible and performant aligner and read mapper☆99Updated this week
- Rapid & standardized genome annotation using protein structural information☆71Jul 2, 2026Updated 3 weeks ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- syncmer graphs, and perhaps other sorts of sequence graphs☆42Jul 10, 2026Updated 2 weeks ago
- COBS - Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams)☆21Nov 24, 2024Updated last year
- A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.☆37Jul 21, 2025Updated last year
- Viral genome coverage evaluation for metagenomic diagnostics☆27Jul 9, 2026Updated 2 weeks ago
- Bitpacked sequence trait and implementation☆19Jul 7, 2026Updated 2 weeks ago
- Python package for detection of chimerism and contamination in prokaryotic genomes.☆93May 11, 2026Updated 2 months ago
- An R Package for Integrated Analysis and Visualization of Microbiome Data☆19May 7, 2026Updated 2 months ago