A fast constructor of the compressed de Bruijn graph from many genomes
☆42Nov 27, 2025Updated 3 months ago
Alternatives and similar repositories for TwoPaCo
Users that are interested in TwoPaCo are comparing it to the libraries listed below
Sorting:
- ☆24Apr 2, 2021Updated 4 years ago
- An efficient index for the colored, compacted, de Bruijn graph☆111Oct 7, 2024Updated last year
- De novo genome assembler.☆11Jul 30, 2018Updated 7 years ago
- Tool (experimental) to compute layout from overlaps with spectral algorithm☆11Nov 28, 2017Updated 8 years ago
- BWT-based index for graphs☆73Mar 12, 2025Updated 11 months ago
- de Bruijn Graph-based read aligner☆35Sep 3, 2018Updated 7 years ago
- Cosmo is a fast, low-memory DNA assembler using a Succinct (variable order) de Bruijn Graph.☆53Mar 12, 2024Updated last year
- a toolset for efficient analysis of 10X Genomics linked read data sets, in particular for de novo assembly☆15Nov 27, 2019Updated 6 years ago
- nimble aligner that will map your reads to the references on a laptop☆11Jun 29, 2017Updated 8 years ago
- Paired reads mapping on de Bruijn graph☆13Jan 15, 2019Updated 7 years ago
- The Dagstuhl Format for Assembly☆13Oct 16, 2017Updated 8 years ago
- Histosketching Using Little Kmers☆56May 25, 2023Updated 2 years ago
- EXPERIMENTAL implementation of side graph☆10Apr 16, 2015Updated 10 years 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
- StriDe Assembler☆25Nov 23, 2017Updated 8 years ago
- semi-reference-based short read compression☆11Mar 5, 2019Updated 6 years ago
- Classify sequencing reads using MinHash.☆48Apr 6, 2020Updated 5 years ago
- Accurate, Lightweight Clustering of de novo Transcriptomes using Fragment Equivalence Classes☆31Jun 16, 2024Updated last year
- Ococo: the first online variant and consensus caller. Call genomic consensus directly from an unsorted SAM/BAM stream.☆46Jan 18, 2019Updated 7 years ago
- de Bruijn Graph REAd mapping Tool☆14Jul 12, 2017Updated 8 years ago
- Johns Hopkins University student-led genomics paper discussion group☆13Apr 19, 2020Updated 5 years ago
- Fast and accurate set similarity estimation via containment min hash☆42Jul 19, 2024Updated last year
- A C++ library and utilities for manipulating the Graphical Fragment Assembly format.☆55May 17, 2022Updated 3 years ago
- Practical Dynamic de Bruijn Graphs☆18Oct 1, 2020Updated 5 years ago
- De novo genome assembly and multisample variant calling☆112Mar 28, 2019Updated 6 years ago
- Graph based multi genome aligner☆49Sep 17, 2021Updated 4 years ago
- COBS - Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams)☆88Jan 25, 2024Updated 2 years ago
- deBGR: An Efficient and Near-Exact Representation of the Weighted de Bruijn Graph☆31Jan 19, 2021Updated 5 years ago
- High-level API for storing and querying sequence variant data☆20May 24, 2019Updated 6 years ago
- Improved multi-sample transcript abundance estimates using adaptive priors☆20Oct 29, 2018Updated 7 years ago
- A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences.☆53Updated this week
- De novo estimates of genetic relatedness from next-gen sequencing data☆45Jul 28, 2019Updated 6 years ago
- Squeakr: An Exact and Approximate k -mer Counting System☆86Feb 23, 2025Updated last year
- ☆15Apr 6, 2016Updated 9 years ago
- This repo is deprecated. Please use gfatools instead.☆15Aug 17, 2018Updated 7 years ago
- efficient alignment of strings to partially ordered string graphs☆33Jan 31, 2022Updated 4 years ago
- Scaffolding genomes using synthetic long read clouds☆20Oct 11, 2016Updated 9 years ago
- A hash map using the BooPHF perfect hash function☆13Sep 25, 2016Updated 9 years ago