A fast multi-threaded k-mer counter
☆539Mar 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☆333May 8, 2026Updated 2 weeks ago
- Fast genome analysis from unassembled short reads☆320Apr 8, 2024Updated 2 years ago
- Mummer alignment tool☆560Feb 4, 2025Updated last year
- The K-mer Analysis Toolkit (KAT) contains a number of tools that analyse and compare K-mer spectra.☆227Nov 25, 2022Updated 3 years ago
- k-mer based assembly evaluation☆343Updated this week
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- Reference-free profiling of polyploid genomes☆145Oct 2, 2025Updated 7 months ago
- A versatile pairwise aligner for genomic and spliced nucleotide sequences☆2,188May 19, 2026Updated last week
- Genome assembly evaluation tool☆510Nov 14, 2024Updated last year
- Next generation sequencing reads de novo assembler.☆240Sep 20, 2025Updated 8 months ago
- Ultrafast de novo assembly for long noisy reads (though having no consensus step)☆353Jul 19, 2025Updated 10 months ago
- Program for aligning DNA sequences, a pairwise aligner.☆249Updated this week
- Tools for manipulating sequence graphs in the GFA and rGFA formats☆250Dec 16, 2025Updated 5 months ago
- De novo assembler for single molecule sequencing reads using repeat graphs☆933Apr 3, 2026Updated last month
- Fast and accurate de novo assembler for long reads☆402May 10, 2024Updated 2 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.
- A single molecule sequence assembler for genomes large and small.☆700Feb 24, 2026Updated 3 months ago
- Pilon is an automated genome assembly improvement and variant detection tool☆381Apr 10, 2022Updated 4 years ago
- Toolkit for processing sequences in FASTA/Q formats☆1,540Jun 1, 2025Updated 11 months ago
- a Bioinformatics Application for Navigating De novo Assembly Graphs Easily☆670Dec 3, 2022Updated 3 years ago
- Yet another k-mer analyzer☆172Dec 30, 2025Updated 4 months ago
- Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)☆1,741Mar 22, 2025Updated last year
- 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 2 years ago
- Graph-based alignment (Hierarchical Graph FM index)☆537Jan 27, 2026Updated 3 months ago
- 3D de novo assembly (3D DNA) pipeline☆225Nov 29, 2023Updated 2 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.
- Hifiasm: a haplotype-resolved assembler for accurate Hifi reads☆775May 15, 2026Updated last week
- An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)☆2,366Apr 24, 2026Updated last month
- haplotypic duplication identification tool☆286Oct 30, 2025Updated 6 months ago
- Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly☆529Sep 27, 2023Updated 2 years ago
- GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more☆480Apr 10, 2026Updated last month
- LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also…☆215May 12, 2026Updated 2 weeks ago
- A genomic k-mer counter (and sequence utility) with nice features.☆166Jul 4, 2025Updated 10 months ago
- bedtools - the swiss army knife for genome arithmetic☆1,036Mar 11, 2025Updated last year
- Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and O…☆391Apr 22, 2026Updated last month
- Proton VPN Special Offer - Get 70% off • AdSpecial partner offer. Trusted by over 100 million users worldwide. Tested, Approved and Recommended by Experts.
- De-Novo Repeat Discovery Tool☆237May 5, 2026Updated 3 weeks ago
- Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads☆240Dec 29, 2023Updated 2 years ago
- Synteny and Rearrangement Identifier☆468Updated this week
- ☆275Jun 26, 2025Updated 11 months ago
- Fast genome and metagenome distance estimation using MinHash☆443Sep 19, 2025Updated 8 months ago
- Classifier for metagenomic sequences☆274Apr 15, 2026Updated last month
- ☆286Dec 29, 2025Updated 4 months ago