A fast multi-threaded k-mer counter
☆534Mar 20, 2024Updated 2 years ago
Alternatives and similar repositories for Jellyfish
Users that are interested in Jellyfish are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Fast and frugal disk based k-mer counter☆328Mar 10, 2026Updated last month
- Fast genome analysis from unassembled short reads☆318Apr 8, 2024Updated 2 years ago
- Mummer alignment tool☆554Feb 4, 2025Updated last year
- The K-mer Analysis Toolkit (KAT) contains a number of tools that analyse and compare K-mer spectra.☆226Nov 25, 2022Updated 3 years ago
- k-mer based assembly evaluation☆341Jun 28, 2024Updated last year
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- Reference-free profiling of polyploid genomes☆144Oct 2, 2025Updated 6 months ago
- A versatile pairwise aligner for genomic and spliced nucleotide sequences☆2,154Updated this week
- Genome assembly evaluation tool☆508Nov 14, 2024Updated last year
- Next generation sequencing reads de novo assembler.☆239Sep 20, 2025Updated 6 months ago
- Ultrafast de novo assembly for long noisy reads (though having no consensus step)☆354Jul 19, 2025Updated 8 months ago
- Program for aligning DNA sequences, a pairwise aligner.☆243Mar 27, 2026Updated 2 weeks ago
- Tools for manipulating sequence graphs in the GFA and rGFA formats☆248Dec 16, 2025Updated 3 months ago
- De novo assembler for single molecule sequencing reads using repeat graphs☆915Apr 3, 2026Updated last week
- Fast and accurate de novo assembler for long reads☆401May 10, 2024Updated last year
- Deploy open-source AI quickly and easily - Bonus Offer • AdRunpod Hub is built for open source. One-click deployment and autoscaling endpoints without provisioning your own infrastructure.
- A single molecule sequence assembler for genomes large and small.☆700Feb 24, 2026Updated last month
- Pilon is an automated genome assembly improvement and variant detection tool☆380Apr 10, 2022Updated 4 years ago
- Toolkit for processing sequences in FASTA/Q formats☆1,534Jun 1, 2025Updated 10 months ago
- a Bioinformatics Application for Navigating De novo Assembly Graphs Easily☆669Dec 3, 2022Updated 3 years ago
- Yet another k-mer analyzer☆166Dec 30, 2025Updated 3 months ago
- Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr…☆297May 9, 2024Updated last year
- Graph-based alignment (Hierarchical Graph FM index)☆532Jan 27, 2026Updated 2 months ago
- 3D de novo assembly (3D DNA) pipeline☆223Nov 29, 2023Updated 2 years ago
- Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)☆1,726Mar 22, 2025Updated last year
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- Hifiasm: a haplotype-resolved assembler for accurate Hifi reads☆764Mar 18, 2025Updated last year
- An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)☆2,324Apr 8, 2026Updated last week
- haplotypic duplication identification tool☆280Oct 30, 2025Updated 5 months ago
- Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly☆531Sep 27, 2023Updated 2 years ago
- GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more☆471Updated this week
- LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also…☆214Mar 9, 2026Updated last month
- A genomic k-mer counter (and sequence utility) with nice features.☆165Jul 4, 2025Updated 9 months ago
- bedtools - the swiss army knife for genome arithmetic☆1,027Mar 11, 2025Updated last year
- Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and O…☆387Updated this week
- 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.
- De-Novo Repeat Discovery Tool☆236Jul 21, 2025Updated 8 months ago
- Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads☆239Dec 29, 2023Updated 2 years ago
- Synteny and Rearrangement Identifier☆460Mar 17, 2026Updated 3 weeks ago
- ☆273Jun 26, 2025Updated 9 months ago
- Fast genome and metagenome distance estimation using MinHash☆438Sep 19, 2025Updated 6 months ago
- Classifier for metagenomic sequences☆272Jun 20, 2025Updated 9 months ago
- ☆286Dec 29, 2025Updated 3 months ago