AdmiralenOla / ScoaryView external linksLinks
Pan-genome wide association studies
☆207May 29, 2024Updated last year
Alternatives and similar repositories for Scoary
Users that are interested in Scoary are comparing it to the libraries listed below
Sorting:
- Rapid large-scale prokaryote pan genome analysis☆369Nov 3, 2025Updated 3 months ago
- Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins☆211Aug 27, 2025Updated 5 months ago
- an interactive viewer for populations of bacterial genomes linked by a phylogeny☆131Feb 26, 2024Updated last year
- ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes☆120May 21, 2024Updated last year
- Interactive, web tool for exploring pan-genome of bacterial strains☆49Jan 14, 2026Updated last month
- Pairwise SNP distance matrix from a FASTA sequence alignment☆153Dec 31, 2025Updated last month
- Locus and lineage tests for bacterial GWAS☆28Oct 5, 2017Updated 8 years ago
- An updated pipeline for pangenome investigation☆341Jan 15, 2026Updated last month
- Build a partitioned pangenome graph from microbial genomes☆293Dec 17, 2025Updated 2 months ago
- Pipeline for analysing intergenic regions in bacteria☆39Oct 25, 2019Updated 6 years ago
- SEER, reimplemented in python 🐍🔮☆130May 22, 2025Updated 8 months ago
- Scan contig files against PubMLST typing schemes☆266Jan 2, 2026Updated last month
- Bayesian inference of ancestral dates on bacterial phylogenetic trees☆94Dec 9, 2025Updated 2 months ago
- Mass screening of contigs for antimicrobial and virulence genes☆475Jan 31, 2026Updated 2 weeks ago
- ☆82Jan 16, 2026Updated last month
- Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.☆186Feb 6, 2026Updated last week
- Rapid haploid variant calling and core genome alignment☆565Dec 12, 2025Updated 2 months ago
- Rapid & standardized annotation of bacterial genomes, MAGs & plasmids☆606Feb 9, 2026Updated last week
- Create a tree using Mash distances☆182Oct 24, 2023Updated 2 years ago
- Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can b…☆149Oct 2, 2025Updated 4 months ago
- hybrid assembly pipeline for bacterial genomes☆632Jul 25, 2024Updated last year
- In this repo you will find demos and tutorials prepared by members of the CBIB. Feel free to use them for non-commercial activities given…☆84Apr 1, 2018Updated 7 years ago
- Evaluation and polishing workflows for T2T genome assemblies☆146Jul 7, 2025Updated 7 months ago
- A tool for generating consensus long-read assemblies for bacterial genomes☆339Sep 11, 2025Updated 5 months ago
- treeWAS: A Phylogenetic Tree-Based Tool for Genome-Wide Association Studies in Microbes☆106Feb 6, 2025Updated last year
- Gene cluster comparison figure generator☆635Dec 22, 2025Updated last month
- Antimicrobial Resistance Identification By Assembly☆184Oct 12, 2023Updated 2 years ago
- "Reads to report" for public health and clinical microbiology☆143Dec 9, 2025Updated 2 months ago
- Making whole bacterial genome sequencing data analysis easy☆114Apr 22, 2025Updated 9 months ago
- Processing pipeline for pan-genome visulization and exploration☆143Oct 9, 2023Updated 2 years ago
- post processing of bacterial pangenome gene presence/absence matrices☆63Jan 19, 2026Updated 3 weeks ago
- Calculate genome wide average nucleotide identity (gwANI) for a multiFASTA alignment☆16Dec 5, 2018Updated 7 years ago
- PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)☆103Feb 9, 2026Updated last week
- Comparison of multiple long read datasets☆155Dec 2, 2025Updated 2 months ago
- Fast genome and metagenome distance estimation using MinHash☆434Sep 19, 2025Updated 4 months ago
- A toolbox for pangenome analysis and threshold evaluation.☆99Jul 8, 2022Updated 3 years ago
- Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads☆235Dec 29, 2023Updated 2 years ago
- A set of scripts for calculating pairwise SNP distance☆44Jan 22, 2023Updated 3 years ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆21Feb 15, 2019Updated 7 years ago