Pan-genome Seed Index
☆20Mar 12, 2025Updated 11 months ago
Alternatives and similar repositories for psi
Users that are interested in psi are comparing it to the libraries listed below
Sorting:
- 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
- Parallel Sequence to Graph Alignment☆36Nov 26, 2022Updated 3 years ago
- BlastGraph is a new tool for computing intensive approximate pattern matching in a sequence graph or a de-Bruijn graph. Given an oriented…☆12May 9, 2013Updated 12 years ago
- Graph-based mapping of long sequences, noisy or HiFi.☆55Oct 5, 2020Updated 5 years ago
- ☆12Sep 7, 2019Updated 6 years ago
- ☆24Apr 2, 2021Updated 4 years ago
- C++ library for analysing and storing large-scale cohorts of sequence variant data☆17Aug 27, 2019Updated 6 years ago
- Minhash Index Extended to Knead Kmer Intersection☆11Mar 18, 2020Updated 5 years ago
- reference free variant assembly☆34Jul 14, 2023Updated 2 years ago
- Generate kmers/minimizers/hashes/MinHash signatures, including with multiple kmer sizes.☆24Jan 9, 2021Updated 5 years ago
- Alignment algorithm for short Illumina reads to a de Bruijn graph☆17Jun 4, 2019Updated 6 years ago
- A cheatsheet for most common Stringology tasks☆14Apr 14, 2021Updated 4 years ago
- ☆15Mar 9, 2018Updated 7 years ago
- ☆18Nov 21, 2024Updated last year
- Pan-genome inference and genotyping with long noisy or short accurate reads☆119Dec 13, 2024Updated last year
- Extremely fast inplace radix sort☆43Jan 31, 2020Updated 6 years ago
- SUPBUB is a tool that, in linear time, finds out superbubbles(special graph-structures) in a directed graph.☆12Sep 19, 2019Updated 6 years ago
- Kmer based genotyper for short reads.☆23Oct 19, 2021Updated 4 years ago
- Practical Dynamic de Bruijn Graphs☆18Oct 1, 2020Updated 5 years ago
- ☆20Aug 18, 2020Updated 5 years ago
- dEploid is designed for deconvoluting mixed genomes with unknown proportions. Traditional ‘phasing’ programs are limited to diploid organ…☆21Jan 20, 2025Updated last year
- Lift-over alignments from variant-aware references☆34Mar 4, 2023Updated 3 years ago
- MONI: A Pangenomic Index for Finding MEMs☆37Mar 25, 2025Updated 11 months ago
- a GFA toolkit☆13Oct 4, 2024Updated last year
- ☆11Aug 2, 2025Updated 7 months ago
- A script to extract graph structure from multiple sequence alignment result and output as GFA/JSON for vg☆11Mar 27, 2019Updated 6 years ago
- Graph based multi genome aligner☆49Sep 17, 2021Updated 4 years ago
- a toolset for fast DNA read set matching and assembly using a new type of reduced kmer☆37Aug 4, 2021Updated 4 years ago
- Code for the paper Aligning Distant Sequences to Graphs using Long Seed Sketches.☆13Nov 1, 2022Updated 3 years ago
- Small utility to quickly find size and GC content of a fasta file. Can also extract sequence. Who doesn't like QUICK and DIRTY!☆13Aug 27, 2018Updated 7 years ago
- Layout module for raw de novo genome assembly of long uncorrected reads.☆21Feb 2, 2021Updated 5 years ago
- BELLA: a Computationally-Efficient and Highly-Accurate Long-Read to Long-Read Aligner and Overlapper☆52May 16, 2022Updated 3 years ago
- recompute GFA link overlaps☆25Sep 14, 2022Updated 3 years ago
- ☆28Sep 28, 2024Updated last year
- Sensitive and Fast Alignment Search Tool for Long Read sequencing Data.☆40Jul 15, 2019Updated 6 years ago
- find likely coding segments in DNA using composition-normalised hexamer tables☆18Oct 18, 2024Updated last year
- Efficient C functions to compute the summary statistics (flagstats) for sequencing read sets.☆15Dec 16, 2019Updated 6 years ago
- genome variation graphs constructed from HLA GRCh38 ALTs☆23Dec 24, 2021Updated 4 years ago