Fast Approximate Pattern Matching using Search Schemes
☆16Jan 14, 2026Updated last month
Alternatives and similar repositories for columba
Users that are interested in columba are comparing it to the libraries listed below
Sorting:
- Parallel Construction of Suffix Arrays in Rust☆26May 2, 2025Updated 10 months ago
- Rapid estimation of phylogenetic trees using sketching☆13Feb 18, 2025Updated last year
- LMS algorithm for computing edit distance with SIMD optimizations☆11Mar 25, 2024Updated last year
- Just another minhash implementation.☆12Feb 23, 2026Updated last week
- A JBrowse plugin for creating sashimi or junction style plots from RNA-seq data☆14Apr 30, 2021Updated 4 years ago
- Rust implementation of probminhash, superminhash and hyperloglog sketching algorithms☆31Jan 22, 2026Updated last month
- Multiple sequence alignment browser☆11Dec 12, 2022Updated 3 years ago
- Compacted and colored de Bruijn graph construction and querying☆92Updated this week
- Pangenome graphs visualisation, distance computing, reconstruction of sequences and other utility functions☆36May 14, 2025Updated 9 months ago
- A Benchmark of Minimal Perfect Hash Function Algorithms.☆38Dec 20, 2022Updated 3 years ago
- GPU implementation of the Wavefront Alignment Algorithm for global, gap-affine, pairwise sequence alginment☆40Apr 30, 2025Updated 10 months ago
- Mapping NCBI Genbank accession to GTDB accession☆14Feb 13, 2021Updated 5 years ago
- JBrowse 1.x Plugin Registry☆14Sep 10, 2023Updated 2 years ago
- mreps: software for tandem repeat identification in DNA☆15Nov 13, 2019Updated 6 years ago
- GFA parser in Rust☆30May 26, 2023Updated 2 years ago
- Hardware Accelerated Read Until☆17Sep 30, 2025Updated 5 months ago
- ☆17Jul 25, 2025Updated 7 months ago
- Host depletion optimised for clinical metagenomic sequencing applications☆16Nov 18, 2024Updated last year
- ☆18May 10, 2023Updated 2 years ago
- Phased structural variant discovery in pangenomes☆39Dec 9, 2025Updated 2 months ago
- PanPA is a tool for building panproteome graphs and aligning sequences back to the graphs.☆18Feb 2, 2025Updated last year
- Cache-friendly, Parallel, and Samplesort-based Constructor for Suffix Arrays and LCP Arrays☆17Jun 23, 2025Updated 8 months ago
- Shared k-mer content between two genomes☆19Jun 21, 2023Updated 2 years ago
- ☆16May 22, 2023Updated 2 years ago
- Fast and Memory Efficient Genome Sketching via HyperLogLog, HyperMinHash and UltraLogLog☆19Jan 22, 2026Updated last month
- Basecalling configuration prediction through FASTQ files☆33Nov 24, 2025Updated 3 months ago
- Repository of the integrated mouse gut metagenomic catalog☆20Mar 14, 2022Updated 3 years ago
- A pipeline for making SWIft Genomes in a Graph (SWIGG) using k-mers☆22Nov 22, 2019Updated 6 years ago
- ☆21Jul 12, 2016Updated 9 years ago
- Code for the paper Succinct k-mer Set Representations Using Subset Rank Queries on the Spectral Burrows-Wheeler Transform (SBWT)☆24Mar 13, 2025Updated 11 months ago
- A tool in order to accurately remove primer sequences from NGS reads in an amplicon experiment☆20Nov 12, 2025Updated 3 months ago
- ☆46Nov 21, 2025Updated 3 months ago
- A Python interface to gb-io, a fast GenBank parser written in Rust.☆24Feb 23, 2026Updated last week
- FMSI is a highly memory efficient exact k-mer set index based on masked superstrings and the masked Burrows-Wheeler transform☆23Nov 20, 2025Updated 3 months ago
- annotation pipeline for microbial genomes and metagenomes☆18Feb 23, 2018Updated 8 years ago
- Metagenomic binning using low-density hashing a support vector machine☆20Oct 2, 2020Updated 5 years ago
- Grinder is a versatile open-source bioinformatic tool to create simulated omic shotgun and amplicon sequence libraries for all main seque…☆18Aug 30, 2018Updated 7 years ago
- Docker images of bioinformatics software☆21Jun 15, 2017Updated 8 years ago
- A deep learning-based SNP calling method to identify SNPs based on low-coverage Nanopore sequencing reads.☆21Nov 20, 2022Updated 3 years ago