Code examples of fast and simple k-mer counters for tutorial purposes
☆175Mar 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 last year
- Global alignment and alignment extension☆143Jun 27, 2023Updated 3 years ago
- a toolset for fast DNA read set matching and assembly using a new type of reduced kmer☆36Aug 4, 2021Updated 5 years ago
- Wavefront alignment algorithm (WFA): Fast and exact gap-affine pairwise alignment☆199Mar 8, 2022Updated 4 years ago
- alignment to variation graph inducer☆164Jul 29, 2026Updated 2 weeks 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.
- A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)☆171May 28, 2024Updated 2 years ago
- base-accurate DNA sequence alignments using WFA and mashmap3☆222Aug 9, 2026Updated last week
- A fast K-mer counter for high-fidelity shotgun datasets☆147Jan 19, 2026Updated 6 months ago
- Sequence-to-graph mapper and graph generator☆485Aug 11, 2025Updated last year
- ☆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☆531Sep 27, 2023Updated 2 years ago
- Yet another k-mer analyzer☆175Dec 30, 2025Updated 7 months ago
- De novo genome assembly and multisample variant calling☆113Mar 28, 2019Updated 7 years 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.
- Fast and frugal disk based k-mer counter☆338Jul 7, 2026Updated last month
- SAPLING: Suffix Array Piecewise Linear INdex for Genomics☆25Sep 1, 2020Updated 5 years ago
- The Modular Aligner and The Modular SV Caller☆47Jul 18, 2023Updated 3 years ago
- A fast approximate aligner for long DNA sequences☆289Oct 11, 2024Updated last year
- Bifrost: Highly parallel construction and indexing of colored and compacted de Bruijn graphs☆226Aug 11, 2026Updated last week
- Peregrine: Fast Genome Assembler Using SHIMMER Index☆102Feb 6, 2022Updated 4 years ago
- Tools for manipulating sequence graphs in the GFA and rGFA formats☆253Dec 16, 2025Updated 8 months ago
- ☆290Dec 29, 2025Updated 7 months ago
- URMAP ultra-fast read mapper☆38Jun 15, 2020Updated 6 years ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- SRF: Satellite Repeat Finder☆108Jan 8, 2024Updated 2 years ago
- Implicit Interval Tree with Interpolation Index☆43Jul 13, 2022Updated 4 years ago
- recompute GFA link overlaps☆26Sep 14, 2022Updated 3 years ago
- Model and predict short DNA sequence features with neural networks☆81Jul 22, 2026Updated 3 weeks ago
- A reimplementation of the WaveFront Alignment algorithm at low memory☆51May 22, 2024Updated 2 years ago
- An efficient index for the colored, compacted, de Bruijn graph☆112Jun 19, 2026Updated last month
- Reference-based variant calling pipeline for a pair of phased haplotype assemblies☆117Jun 6, 2021Updated 5 years ago
- Inference of ploidy and heterozygosity structure using whole genome sequencing data☆298May 28, 2026Updated 2 months ago
- Graph-based mapping of long sequences, noisy or HiFi.☆55Oct 5, 2020Updated 5 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.
- minimizer-space de Bruijn graphs (mdBG) for whole genome assembly☆184Sep 19, 2024Updated last year
- Assembled Genomes Compressor☆187Jul 22, 2026Updated 3 weeks ago
- Self-contained, multi-threaded fasta/q parser☆50Mar 10, 2026Updated 5 months ago
- Gfapy: a flexible and extensible software library for handling sequence graphs in Python☆71Nov 13, 2025Updated 9 months ago
- ☆198Feb 10, 2026Updated 6 months ago
- Minhash Index Extended to Knead Kmer Intersection☆11Mar 18, 2020Updated 6 years ago
- Fast and accurate genomic distances using HyperLogLog☆162Jan 19, 2023Updated 3 years ago