pesho-ivanov / minSHLinks
A minimal Python re-implementation of the A* with seed heuristic for exact global alignment (edit distance) in near-linear time
☆22Updated 11 months ago
Alternatives and similar repositories for minSH
Users that are interested in minSH are comparing it to the libraries listed below
Sorting:
- Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads☆17Updated 5 years ago
- AStarix: Fast and Optimal Sequence-to-Graph Aligner☆74Updated 3 years ago
- A python library for efficient KNN search within metric spaces using multiple distance functions.☆14Updated last year
- TreeSwift: Fast tree module for Python 3☆84Updated 11 months ago
- Minhash and maxhash library in Python, combining flexibility, expressivity, and performance.☆22Updated 10 months ago
- Align sequences and then parse features.☆17Updated 2 weeks ago
- toolkit for file system virtualisation of random access compressed FASTA, FAI, DICT & TWOBIT files☆22Updated last year
- Catalogue of pairwise alignment algorithms and benchmarks☆24Updated last year
- VCF Observer is a VCF file analysis, comparison, and visualization tool.☆18Updated 10 months ago
- A fast, AVX2 and ARM Neon accelerated FM index library☆35Updated 11 months ago
- Tools and utilities for running Dockerized metagenomics tools in the Cloud☆22Updated 6 years ago
- Pandas DataFrames for phylogenetics☆74Updated 4 years ago
- Construct a Physical Map from Linked Reads☆18Updated last year
- A repository for the GenGraph toolkit for the creation and manipulation of graph genomes☆51Updated 4 years ago
- Code accompanying the publication for compressed graph annotation☆13Updated 6 years ago
- Sequence Distance Graph framework: graph + reads + mapping + analysis☆25Updated 3 years ago
- Analyzes whole genome sequencing data for gene-editing verification☆10Updated 2 weeks ago
- Orpheum (Previously called and published under sencha) is a Python package for directly translating RNA-seq reads into coding protein seq…☆18Updated 3 years ago
- A fast seed-embed-extend based sequence mapper and aligner☆23Updated last year
- Deep learning-based prediction of regulatory genome sequences☆12Updated 5 years ago
- A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences.☆53Updated last week
- A tool for simulating random mutations in any genome☆42Updated last year
- Proof-of-concept implementation of GWFA for sequence-to-graph alignment☆55Updated last year
- The PanGenome Graph Builder☆16Updated last year
- Experimental plugin to integrate GPT like prompt into Nextflow☆16Updated last year
- The NCBI SARS-CoV-2 Variant Calling (SC2VC) Pipeline allows calling high-confidence variants from SARS-CoV-2 NGS data in a standardized f…☆14Updated 2 years ago
- Scalable annotated de Bruijn graphs for DNA indexing, alignment, and assembly☆188Updated this week
- Refinements of the WFA alignment algorithm with better complexity☆26Updated 3 years ago
- Pairwise nucleotide alignment benchmark of Rust bindings☆30Updated 2 years ago
- Given a set of kmers (fasta format) and a set of sequences (fasta format), this tool will extract the sequences containing the kmers.☆21Updated 2 years ago