Martinsos / edlibLinks
Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
☆579Updated 8 months ago
Alternatives and similar repositories for edlib
Users that are interested in edlib are comparing it to the libraries listed below
Sorting:
- ☆314Updated 3 weeks ago
- The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.☆446Updated 2 weeks ago
- SeqAn's official repository.☆499Updated last month
- Pairwise Sequence Alignment Library☆275Updated 5 months ago
- A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)☆170Updated last year
- Bifrost: Highly parallel construction and indexing of colored and compacted de Bruijn graphs☆222Updated 3 months ago
- A fast multi-threaded k-mer counter☆529Updated last year
- FM-Index full-text index implementation using RRR Wavelet trees (libcds) and fast suffix sorting (libdivsufsort) including experimental r…☆109Updated 11 years ago
- Code examples of fast and simple k-mer counters for tutorial purposes☆171Updated 5 years ago
- SIMD partial order alignment tool/library☆171Updated 4 months ago
- WFA-lib: Wavefront alignment algorithm library v2☆208Updated this week
- An ultrafast memory-efficient short read aligner☆266Updated 3 years ago
- C library for high-throughput sequencing data formats☆904Updated this week
- A fast approximate aligner for long DNA sequences☆286Updated last year
- Wavefront alignment algorithm (WFA): Fast and exact gap-affine pairwise alignment☆199Updated 3 years ago
- Graphical Fragment Assembly (GFA) Format Specification☆218Updated last year
- NVBIO is a library of reusable components designed to accelerate bioinformatics applications using CUDA.☆225Updated 5 years ago
- NCLS. Basically a static interval-tree that is silly fast for both construction and lookups. Deprecated but maintained.☆224Updated 7 months ago
- C++ Implementations of sketch data structures with SIMD Parallelism, including Python bindings☆158Updated last year
- Fast, portable C implementations of Needleman-Wunsch and Smith-Waterman sequence alignment☆97Updated 4 years ago
- ☆284Updated last month
- Sequence-to-graph mapper and graph generator☆470Updated 5 months ago
- Efficient pythonic random access to fasta subsequences☆482Updated 5 months ago
- a minimal C++ interval tree implementation☆237Updated 4 years ago
- SIMD C/C++ library for massive optimal sequence alignment (local/SW, infix, overlap, global)☆39Updated 2 years ago
- A PyTorch Basecaller for Oxford Nanopore Reads☆428Updated 3 weeks ago
- DeepConsensus uses gap-aware sequence transformers to correct errors in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS) …☆255Updated 10 months ago
- C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings☆666Updated 3 months ago
- Global alignment and alignment extension☆142Updated 2 years ago
- Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data☆297Updated 5 months ago