SIMD partial order alignment tool/library
☆176Sep 21, 2025Updated 6 months ago
Alternatives and similar repositories for spoa
Users that are interested in spoa are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- abPOA: an SIMD-based C library for fast partial order alignment using adaptive band☆136Feb 22, 2026Updated last month
- Global alignment and alignment extension☆142Jun 27, 2023Updated 2 years ago
- ☆286Dec 29, 2025Updated 2 months ago
- WFA-lib: Wavefront alignment algorithm library v2☆210Updated this week
- Refinements of the WFA alignment algorithm with better complexity☆26Mar 31, 2022Updated 3 years ago
- ☆315Jan 15, 2026Updated 2 months ago
- Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads☆239Dec 29, 2023Updated 2 years ago
- Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.☆584May 13, 2025Updated 10 months ago
- SIMD-parallel BLAST X-drop DP on sequence graphs☆24May 30, 2024Updated last year
- Wavefront alignment algorithm (WFA): Fast and exact gap-affine pairwise alignment☆199Mar 8, 2022Updated 4 years ago
- Long read aligner☆114May 26, 2023Updated 2 years ago
- A simple Partial Order Aligner based on Lee, Grasso and Sharlow (2002), for education/demonstration purposes☆75Jun 20, 2024Updated last year
- A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)☆170May 28, 2024Updated last year
- Rust bindings to the wavefront algorithm C implementation☆17Sep 20, 2022Updated 3 years ago
- Python bindings to spoa☆22Dec 3, 2025Updated 3 months ago
- Assembled Genomes Compressor☆178Nov 25, 2024Updated last year
- A fast approximate aligner for long DNA sequences☆287Oct 11, 2024Updated last year
- ☆11Dec 9, 2022Updated 3 years ago
- base-accurate DNA sequence alignments using edlib and mashmap2☆32Feb 15, 2021Updated 5 years ago
- A reimplementation of the WaveFront Alignment algorithm at low memory☆50May 22, 2024Updated last year
- Peregrine: Fast Genome Assembler Using SHIMMER Index☆102Feb 6, 2022Updated 4 years ago
- GBWT-based handle graph☆31Updated this week
- Bidirectional WFA (Paper)☆49May 20, 2024Updated last year
- Sensitive and Fast Alignment Search Tool for Long Read sequencing Data.☆40Jul 15, 2019Updated 6 years ago
- Pairwise Sequence Alignment Library☆276Aug 27, 2025Updated 6 months ago
- 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
- Graph-based mapping of long sequences, noisy or HiFi.☆55Oct 5, 2020Updated 5 years ago
- Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr…☆297May 9, 2024Updated last year
- De novo clustering of long transcript reads into genes☆70Apr 27, 2025Updated 10 months ago
- Core library of the Genome Analysis Toolbox with de-Bruijn graph☆65Feb 1, 2025Updated last year
- Bifrost: Highly parallel construction and indexing of colored and compacted de Bruijn graphs☆223Oct 23, 2025Updated 5 months ago
- base-accurate DNA sequence alignments using WFA and mashmap3☆212Updated this week
- NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on r…☆308Mar 18, 2024Updated 2 years ago
- A C++ header-only library for reading Oxford Nanopore Fast5 files☆53Jun 27, 2022Updated 3 years ago
- C++ library for parsing several formats in bioinformatics☆10May 18, 2023Updated 2 years ago
- Error correction of ONT transcript reads☆58Sep 6, 2023Updated 2 years ago
- Sequence-to-graph mapper and graph generator☆473Aug 11, 2025Updated 7 months ago
- Header-only, gzread-like reader for gzip, bz2, and xz.☆11Aug 8, 2018Updated 7 years ago
- The Modular Aligner and The Modular SV Caller☆46Jul 18, 2023Updated 2 years ago