Global alignment and alignment extension
☆143Jun 27, 2023Updated 3 years ago
Alternatives and similar repositories for ksw2
Users that are interested in ksw2 are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- efficient alignment of strings to partially ordered string graphs☆33Apr 22, 2026Updated 4 months ago
- Adaptive semi-global banded alignment on string graphs☆66May 4, 2018Updated 8 years ago
- A reimplementation of the WaveFront Alignment algorithm at low memory☆51May 22, 2024Updated 2 years ago
- Pairwise Sequence Alignment Library☆288Aug 27, 2025Updated last year
- Graph-based mapping of long sequences, noisy or HiFi.☆55Oct 5, 2020Updated 5 years ago
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- SIMD partial order alignment tool/library☆183Sep 21, 2025Updated 11 months ago
- A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)☆170May 28, 2024Updated 2 years ago
- Wavefront alignment algorithm (WFA): Fast and exact gap-affine pairwise alignment☆199Mar 8, 2022Updated 4 years ago
- Peregrine: Fast Genome Assembler Using SHIMMER Index☆102Feb 6, 2022Updated 4 years ago
- The Modular Aligner and The Modular SV Caller☆47Jul 18, 2023Updated 3 years ago
- A C++ library and utilities for manipulating the Graphical Fragment Assembly format.☆56May 17, 2022Updated 4 years ago
- ☆321Jan 15, 2026Updated 7 months ago
- ☆11Dec 9, 2022Updated 3 years ago
- Integrated Variant Caller☆17Mar 15, 2018Updated 8 years ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Ococo: the first online variant and consensus caller. Call genomic consensus directly from an unsorted SAM/BAM stream.☆46Jan 18, 2019Updated 7 years ago
- A fast approximate aligner for long DNA sequences☆289Oct 11, 2024Updated last year
- Code examples of fast and simple k-mer counters for tutorial purposes☆175Mar 10, 2020Updated 6 years ago
- Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.☆606May 13, 2025Updated last year
- Incremental construction of FM-index for DNA sequences☆72Jun 12, 2024Updated 2 years ago
- a string to graph aligner☆41Jul 5, 2016Updated 10 years ago
- [IMPORTANT: not for real data analysis, only for algorithm evaluation] fast and accurate alignment tool for PacBio and Nanopore long read…☆124Sep 10, 2018Updated 7 years ago
- Graphical Fragment Assembly (GFA) Format Specification☆222Aug 21, 2024Updated 2 years ago
- AStarix: Fast and Optimal Sequence-to-Graph Aligner☆74Dec 25, 2021Updated 4 years ago
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- This repo is deprecated. Please use gfatools instead.☆15Aug 17, 2018Updated 8 years ago
- Refinements of the WFA alignment algorithm with better complexity☆26Mar 31, 2022Updated 4 years ago
- Proof-of-concept implementation of GWFA for sequence-to-graph alignment☆57May 29, 2024Updated 2 years ago
- Header-only, gzread-like reader for gzip, bz2, and xz.☆11Aug 8, 2018Updated 8 years ago
- An efficient index for the colored, compacted, de Bruijn graph☆112Jun 19, 2026Updated 2 months ago
- Sequence-to-graph mapper and graph generator☆487Aug 11, 2025Updated last year
- a wee tool for random access into BGZF files.☆86May 10, 2018Updated 8 years ago
- Benchmark on adaptive banded algorithm☆19Feb 26, 2023Updated 3 years ago
- Squeakr: An Exact and Approximate k -mer Counting System☆85Feb 23, 2025Updated last year
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Exact Tandem Repeat Finder (not a TRF replacement)☆51Oct 22, 2019Updated 6 years ago
- semi-reference-based short read compression☆11Mar 5, 2019Updated 7 years ago
- De Bruijn graph representation in low memory☆36Jul 6, 2024Updated 2 years ago
- WFA-lib: Wavefront alignment algorithm library v2☆225Aug 7, 2026Updated 3 weeks ago
- Fast and accurate genomic distances using HyperLogLog☆162Jan 19, 2023Updated 3 years ago
- This repo is DEPRECATED. Please use minimap2, the successor of minimap.☆106Sep 20, 2017Updated 8 years ago
- Layout module for raw de novo genome assembly of long uncorrected reads.☆21Feb 2, 2021Updated 5 years ago