gsufsort: building suffix arrays, LCP-arrays and BWTs for string collections [AMB 2020]
☆26Feb 16, 2025Updated last year
Alternatives and similar repositories for gsufsort
Users that are interested in gsufsort are comparing it to the libraries listed below
Sorting:
- Inducing enhanced suffix arrays for string collections [DCC'16, TCS 2017]☆26Dec 2, 2025Updated 3 months ago
- Generalized enhanced suffix array construction in external memory [CPM'13, AMB 2017]☆17Aug 9, 2021Updated 4 years ago
- Implementation of eBWT using Prefix-free parse (PFP)☆14Jul 14, 2025Updated 7 months ago
- Optimal suffix sorting and LCP array construction for constant alphabets [IPL 2017]☆10Aug 17, 2018Updated 7 years ago
- A lightweight suffix-sorting library enhanced with LCP construction☆13Mar 26, 2020Updated 5 years ago
- A cheatsheet for most common Stringology tasks☆14Apr 14, 2021Updated 4 years ago
- BWT Text Indexing Library: a set of tools to work with BWT-based text indexes☆25Apr 25, 2022Updated 3 years ago
- ☆20Dec 13, 2023Updated 2 years ago
- Phylogenetic Clustering (Phyloclustering)☆10Sep 6, 2023Updated 2 years ago
- Run-length compressed BWT with LZ77 sampled suffix array☆10Apr 25, 2022Updated 3 years ago
- A fast and efficient short read mapper☆13Nov 7, 2021Updated 4 years ago
- Lightweight resources assembly algorithm☆19May 17, 2017Updated 8 years ago
- ☆26Aug 10, 2021Updated 4 years ago
- ☆14Oct 29, 2021Updated 4 years ago
- De novo genome assembler.☆11Jul 30, 2018Updated 7 years ago
- genotyping by Mapping-free ALternate-allele detection of known VAriants☆10Mar 6, 2023Updated 3 years ago
- Finding Maximal Exact Matches (MEMs) using a Sampled LCP Array☆10Mar 7, 2024Updated last year
- A python toolkit for building and querying multi-string BWTs☆27Mar 2, 2017Updated 9 years ago
- Finding putative exons and constructing splicegraphs using Trans-ABySS contigs☆11Nov 8, 2018Updated 7 years ago
- A space-efficient compressor based on the Re-Pair grammar☆10Apr 6, 2017Updated 8 years ago
- An R package for Standardized Summary, Annotation, Comparison, and Visualization of CNV, CNVR and ROH☆15Oct 17, 2021Updated 4 years ago
- MEM mapper prototype☆13Nov 28, 2020Updated 5 years ago
- C++20 Generalized Suffix Tree implementation☆13Oct 23, 2022Updated 3 years ago
- a toolkit for evaluation of the lenght of k-mer in a given genome dataset for alignment-free phylogenimic analysis.☆14Nov 21, 2024Updated last year
- ♥ Fast and Accurate Estimation of Evolutionary Distances☆29Apr 14, 2025Updated 10 months ago
- A tool to filter BUSCO output into single-copy gene files for phylogenomics☆13Jul 24, 2024Updated last year
- Online construction of run-length BWT (RLBWT) and r-index. Plus, online LZ77 parsing based on RLBWT.☆14May 11, 2018Updated 7 years ago
- Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens☆37Jan 22, 2026Updated last month
- mitochondrial variant analysis tools☆15Mar 4, 2021Updated 5 years ago
- DNN-based small variant caller☆12May 2, 2022Updated 3 years ago
- A simple C++11 memory monitor☆15Dec 17, 2015Updated 10 years ago
- GERMLINE is an algorithm for inferring long shared segments of Identity by Descent (IBD) between pairs of individuals in a large populati…☆15Apr 5, 2019Updated 6 years 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
- A lightweight suffix-sorting library☆401Mar 25, 2020Updated 5 years ago
- Wavelet tree based on a fixed block boosting technique☆16May 18, 2021Updated 4 years ago
- Fast Neighbor-Joining and other distance-based methods for phylogenetics☆15Jun 21, 2024Updated last year
- An optimal space run-length Burrows-Wheeler transform full-text index☆68May 31, 2023Updated 2 years ago
- A fast, AVX2 and ARM Neon accelerated FM index library☆36Dec 9, 2024Updated last year
- FQSqueezer - FASTQ compressor based on k-mer statistics☆17Feb 24, 2024Updated 2 years ago