Code examples of fast and simple k-mer counters for tutorial purposes
☆172Mar 10, 2020Updated 6 years ago
Alternatives and similar repositories for kmer-cnt
Users that are interested in kmer-cnt are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- REINDEER REad Index for abuNDancE quERy☆56Jul 6, 2025Updated 10 months ago
- Global alignment and alignment extension☆142Jun 27, 2023Updated 2 years ago
- a toolset for fast DNA read set matching and assembly using a new type of reduced kmer☆37Aug 4, 2021Updated 4 years ago
- Wavefront alignment algorithm (WFA): Fast and exact gap-affine pairwise alignment☆198Mar 8, 2022Updated 4 years ago
- alignment to variation graph inducer☆159Apr 11, 2026Updated 3 weeks ago
- End-to-end encrypted cloud storage - Proton Drive • AdSpecial offer: 40% Off Yearly / 80% Off First Month. Protect your most important files, photos, and documents from prying eyes.
- A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)☆170May 28, 2024Updated last year
- base-accurate DNA sequence alignments using WFA and mashmap3☆215Mar 20, 2026Updated last month
- A fast K-mer counter for high-fidelity shotgun datasets☆143Jan 19, 2026Updated 3 months ago
- Sequence-to-graph mapper and graph generator☆477Aug 11, 2025Updated 8 months ago
- ☆24Apr 2, 2021Updated 5 years ago
- A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment☆87Apr 8, 2021Updated 5 years ago
- Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly☆530Sep 27, 2023Updated 2 years ago
- Yet another k-mer analyzer☆171Dec 30, 2025Updated 4 months ago
- De novo genome assembly and multisample variant calling☆112Mar 28, 2019Updated 7 years ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Fast and frugal disk based k-mer counter☆332Updated this week
- The Modular Aligner and The Modular SV Caller☆47Jul 18, 2023Updated 2 years ago
- A fast approximate aligner for long DNA sequences☆287Oct 11, 2024Updated last year
- Bifrost: Highly parallel construction and indexing of colored and compacted de Bruijn graphs☆224Oct 23, 2025Updated 6 months ago
- Tools for manipulating sequence graphs in the GFA and rGFA formats☆250Dec 16, 2025Updated 4 months ago
- Peregrine: Fast Genome Assembler Using SHIMMER Index☆102Feb 6, 2022Updated 4 years ago
- ☆287Dec 29, 2025Updated 4 months ago
- URMAP ultra-fast read mapper☆38Jun 15, 2020Updated 5 years ago
- Implicit Interval Tree with Interpolation Index☆42Jul 13, 2022Updated 3 years ago
- Bare Metal GPUs on DigitalOcean Gradient AI • AdPurpose-built for serious AI teams training foundational models, running large-scale inference, and pushing the boundaries of what's possible.
- SRF: Satellite Repeat Finder☆102Jan 8, 2024Updated 2 years ago
- recompute GFA link overlaps☆26Sep 14, 2022Updated 3 years ago
- A reimplementation of the WaveFront Alignment algorithm at low memory☆51May 22, 2024Updated last year
- An efficient index for the colored, compacted, de Bruijn graph☆112Mar 11, 2026Updated last month
- Inference of ploidy and heterozygosity structure using whole genome sequencing data☆294Feb 25, 2026Updated 2 months ago
- Reference-based variant calling pipeline for a pair of phased haplotype assemblies☆109Jun 6, 2021Updated 4 years ago
- Graph-based mapping of long sequences, noisy or HiFi.☆55Oct 5, 2020Updated 5 years ago
- minimizer-space de Bruijn graphs (mdBG) for whole genome assembly☆183Sep 19, 2024Updated last year
- Gfapy: a flexible and extensible software library for handling sequence graphs in Python☆71Nov 13, 2025Updated 5 months 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.
- Assembled Genomes Compressor☆180Updated this week
- Self-contained, multi-threaded fasta/q parser☆50Mar 10, 2026Updated last month
- ☆189Feb 10, 2026Updated 2 months ago
- Minhash Index Extended to Knead Kmer Intersection☆11Mar 18, 2020Updated 6 years ago
- Long read aligner☆114May 26, 2023Updated 2 years ago
- Fast and accurate genomic distances using HyperLogLog☆162Jan 19, 2023Updated 3 years ago
- A versatile toolkit for k-mers with taxonomic information☆82Aug 28, 2025Updated 8 months ago