jltsiren / gcsa2
BWT-based index for graphs
☆71Updated this week
Related projects ⓘ
Alternatives and complementary repositories for gcsa2
- Adaptive semi-global banded alignment on string graphs☆63Updated 6 years ago
- Cosmo is a fast, low-memory DNA assembler using a Succinct (variable order) de Bruijn Graph.☆51Updated 7 months ago
- Estimating k-mer coverage histogram of genomics data☆76Updated 10 months ago
- Substring index for paths in a graph☆60Updated this week
- Core library of the Genome Analysis Toolbox with de-Bruijn graph☆63Updated last month
- De novo genome assembly and multisample variant calling☆113Updated 5 years ago
- A C++ header-only library for reading Oxford Nanopore Fast5 files☆53Updated 2 years ago
- An efficient index for the colored, compacted, de Bruijn graph☆107Updated last month
- utilities for indexing and sequence extraction from FASTA files☆59Updated 3 years ago
- A C++ library and utilities for manipulating the Graphical Fragment Assembly format.☆51Updated 2 years ago
- Implementation of Positional Burrows-Wheeler Transform for genetic data☆100Updated 7 months ago
- Assembled Genomes Compressor☆154Updated 7 months ago
- Create Bloom filters for a given reference and then use it to categorize sequences☆75Updated last week
- REINDEER REad Index for abuNDancE quERy☆56Updated 3 months ago
- This repo is DEPRECATED. Please use minimap2, the successor of minimap.☆106Updated 7 years ago
- Squeakr: An Exact and Approximate k -mer Counting System☆85Updated 9 months ago
- A tool for merging large BWTs☆26Updated 3 years ago
- abPOA: an SIMD-based C library for fast partial order alignment using adaptive band☆118Updated last week
- Global alignment and alignment extension☆127Updated last year
- Parallel Sequence to Graph Alignment☆35Updated last year
- Gfapy: a flexible and extensible software library for handling sequence graphs in Python☆65Updated 2 weeks ago
- Rapid sensitive and accurate read mapping via quasi-mapping☆89Updated 4 years ago
- Self-contained, multi-threaded fasta/q parser☆43Updated last month
- Standalone C library for assembling Illumina short reads in small regions☆72Updated last year
- Incremental construction of FM-index for DNA sequences☆68Updated 4 months ago
- An Oxford Nanopore Basecaller☆71Updated 3 years ago
- compacted de Bruijn graph construction in low memory☆99Updated last month
- Genome inference from a population reference graph☆93Updated last year
- De novo assembly based variant calling pipeline for Illumina short reads☆107Updated 3 years ago