Building the compacted de Bruijn graph efficiently from references or reads.
☆92Feb 20, 2026Updated last week
Alternatives and similar repositories for cuttlefish
Users that are interested in cuttlefish are comparing it to the libraries listed below
Sorting:
- ProphAsm – a rapid computation of simplitigs directly from k-mer sets☆25Feb 17, 2023Updated 3 years ago
- Compacted and colored de Bruijn graph construction and querying☆92Updated this week
- Contains the description of a file format to store kmers and associated values☆34Aug 17, 2022Updated 3 years ago
- Space-efficient pseudoalignment with a colored de Bruijn graph☆52Mar 13, 2025Updated 11 months ago
- FMSI is a highly memory efficient exact k-mer set index based on masked superstrings and the masked Burrows-Wheeler transform☆23Nov 20, 2025Updated 3 months ago
- Fast, Cache-Efficient, and Scalable Queries on Pangenomes☆36Nov 7, 2025Updated 3 months ago
- Bifrost: Highly parallel construction and indexing of colored and compacted de Bruijn graphs☆222Oct 23, 2025Updated 4 months ago
- De Bruijn graph representation in low memory☆35Jul 6, 2024Updated last year
- Genome inference from a population reference graph☆96Apr 1, 2025Updated 11 months ago
- Improved multi-sample transcript abundance estimates using adaptive priors☆20Oct 29, 2018Updated 7 years ago
- An efficient index for the colored, compacted, de Bruijn graph☆111Oct 7, 2024Updated last year
- REINDEER REad Index for abuNDancE quERy☆56Jul 6, 2025Updated 7 months ago
- Minimum plain text representation of kmer sets☆16Jan 30, 2025Updated last year
- minimizer-space de Bruijn graphs (mdBG) for whole genome assembly☆184Sep 19, 2024Updated last year
- Mantis: A Fast, Small, and Exact Large-Scale Sequence-Search Index☆86Mar 7, 2024Updated last year
- Fast and compact locality-preserving minimal perfect hashing for k-mer sets.☆43Nov 18, 2023Updated 2 years ago
- COBS - Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams)☆88Jan 25, 2024Updated 2 years ago
- A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences.☆53Jan 31, 2026Updated last month
- compacted de Bruijn graph construction in low memory☆100Nov 4, 2025Updated 3 months ago
- Filter of Pairwise Alignement☆44Jan 31, 2022Updated 4 years ago
- BWT construction and search☆126Jan 14, 2026Updated last month
- de Bruijn graph cOrrectiOn from graph aLignment☆11Jul 20, 2020Updated 5 years ago
- Next Index to Query Kmer Intersection☆17Feb 1, 2023Updated 3 years ago
- Dashing 2 is a fast toolkit for k-mer and minimizer encoding, sketching, comparison, and indexing.☆70Jun 17, 2024Updated last year
- Scrooge is a high-performance pairwise sequence aligner based on the GenASM algorithm. Scrooge includes three novel algorithmic improveme…☆38Jun 23, 2023Updated 2 years ago
- Single-Cell RNA-seq pseudo-aligner☆52May 6, 2024Updated last year
- ☆21Dec 26, 2025Updated 2 months ago
- Wavefront alignment algorithm (WFA): Fast and exact gap-affine pairwise alignment☆199Mar 8, 2022Updated 3 years ago
- Assembled Genomes Compressor☆178Nov 25, 2024Updated last year
- ☆14Feb 19, 2026Updated last week
- Software that separates very close sequences that have been collapsed during assembly. Uses only long reads.☆35Apr 23, 2025Updated 10 months ago
- ⚡️ 🧬 Fulgor is a fast and space-efficient colored de Bruijn graph index.☆59Updated this week
- Index kmtricks bf matrices☆46Feb 13, 2026Updated 2 weeks ago
- A fast approximate aligner for long DNA sequences☆286Oct 11, 2024Updated last year
- Reference implementations of minimizer schemes to go with the mod-minimizers paper.☆28Apr 24, 2025Updated 10 months ago
- Unfazed by genomic variant phasing☆27May 26, 2024Updated last year
- Kmer-db is a fast and memory-efficient tool for large-scale k-mer analyses (indexing, querying, estimating evolutionary relationships, et…☆97May 20, 2025Updated 9 months ago
- A Rust library providing fully dynamic sets of k-mers with high locality☆47Feb 12, 2026Updated 2 weeks ago
- Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.☆235Oct 12, 2025Updated 4 months ago