A very fast interval tree data structure
☆131Feb 3, 2025Updated last year
Alternatives and similar repositories for coitrees
Users that are interested in coitrees are comparing it to the libraries listed below
Sorting:
- Implicit Interval Tree with Interpolation Index☆42Jul 13, 2022Updated 3 years ago
- A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)☆170May 28, 2024Updated last year
- Proof-of-concept implementation of GWFA for sequence-to-graph alignment☆56May 29, 2024Updated last year
- Fast and exact gap-affine partial order alignment☆59Feb 3, 2026Updated 3 weeks ago
- ☆21Dec 26, 2025Updated 2 months ago
- base-accurate DNA sequence alignments using WFA and mashmap3☆210Jan 30, 2026Updated last month
- A Rust library and command line tool for working with genomic ranges and their data.☆100May 29, 2024Updated last year
- Efficient, parallel compression for terabyte-scale data☆61Updated this week
- String algorithm visualizations☆13Feb 7, 2023Updated 3 years ago
- A pairwise sequence aligner written in Rust☆145Jan 27, 2026Updated last month
- A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)☆143Aug 24, 2025Updated 6 months ago
- drunk on perbase pileups and lua expressions☆19Nov 15, 2025Updated 3 months ago
- C implementation of the Landau-Vishkin algorithm☆35Apr 8, 2022Updated 3 years ago
- A bit-packed k-mer representation (and relevant utilities) for rust☆47Jun 26, 2024Updated last year
- Pairwise nucleotide alignment benchmark of Rust bindings☆31Jul 27, 2023Updated 2 years ago
- Reference implementations of minimizer schemes to go with the mod-minimizers paper.☆28Apr 24, 2025Updated 10 months ago
- Fast FASTX parsing and k-mer methods in Rust☆210Jan 27, 2026Updated last month
- A SIMD-accelerated library to compute random minimizers☆39Updated this week
- Refinements of the WFA alignment algorithm with better complexity☆26Mar 31, 2022Updated 3 years ago
- SIMD-accelerated library for computing global and X-drop affine gap penalty sequence-to-sequence or sequence-to-profile alignments using …☆139Jun 23, 2024Updated last year
- Efficient C functions to compute the summary statistics (flagstats) for sequencing read sets.☆15Dec 16, 2019Updated 6 years ago
- Compacted and colored de Bruijn graph construction and querying☆92Updated this week
- bioinformatics toolkit in rust☆98Feb 15, 2026Updated 2 weeks ago
- Assembled Genomes Compressor☆178Nov 25, 2024Updated last year
- bedtools-like functionality for interval sets in rust☆55Aug 5, 2025Updated 6 months ago
- using all the bits for echt rapid variant annotation and filtering☆153Feb 18, 2026Updated last week
- Catalogue of pairwise alignment algorithms and benchmarks☆25Jan 6, 2026Updated last month
- A reimplementation of the WaveFront Alignment algorithm at low memory☆50May 22, 2024Updated last year
- WFA-lib: Wavefront alignment algorithm library v2☆209Feb 8, 2026Updated 3 weeks ago
- Grep for FASTQ files☆103Dec 17, 2025Updated 2 months ago
- Hidden Markov Model based Copy number caller☆20Dec 9, 2025Updated 2 months ago
- Iterate over minimizers of a DNA sequence☆31Jul 12, 2024Updated last year
- implicit pangenome graph☆89Updated this week
- gia: Genomic Interval Arithmetic☆66Aug 21, 2024Updated last year
- Wavefront alignment algorithm (WFA): Fast and exact gap-affine pairwise alignment☆199Mar 8, 2022Updated 3 years ago
- A command line tool (in Kotlin/JVM) for intuitively visualizing BAM alignments. (Currently unmaintained)☆11Jan 7, 2024Updated 2 years ago
- Bam Read Index - Extract alignments from a bam file by readname☆28Apr 22, 2024Updated last year
- abPOA: an SIMD-based C library for fast partial order alignment using adaptive band☆135Feb 22, 2026Updated last week
- a toolset for fast DNA read set matching and assembly using a new type of reduced kmer☆37Aug 4, 2021Updated 4 years ago