Pan-genome wide association studies
☆223May 29, 2024Updated 2 years ago
Alternatives and similar repositories for Scoary
Users that are interested in Scoary are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins☆221Aug 27, 2025Updated 11 months ago
- an interactive viewer for populations of bacterial genomes linked by a phylogeny☆133Feb 26, 2024Updated 2 years ago
- Rapid large-scale prokaryote pan genome analysis☆380Nov 3, 2025Updated 9 months ago
- ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes☆127Jun 2, 2026Updated 2 months ago
- Interactive, web tool for exploring pan-genome of bacterial strains☆50Jan 14, 2026Updated 7 months ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Locus and lineage tests for bacterial GWAS☆28Oct 5, 2017Updated 8 years ago
- Pairwise SNP distance matrix from a FASTA sequence alignment☆156Dec 31, 2025Updated 7 months ago
- Pipeline for analysing intergenic regions in bacteria☆39Oct 25, 2019Updated 6 years ago
- An updated pipeline for pangenome investigation☆370Jul 2, 2026Updated last month
- Bayesian inference of ancestral dates on bacterial phylogenetic trees☆99Dec 9, 2025Updated 8 months ago
- SEER, reimplemented in python 🐍🔮☆137Jul 23, 2026Updated 3 weeks ago
- Rapid haploid variant calling and core genome alignment☆595Dec 12, 2025Updated 8 months ago
- Calculate assocations between genes and traits☆32Mar 10, 2025Updated last year
- treeWAS: A Phylogenetic Tree-Based Tool for Genome-Wide Association Studies in Microbes☆108Feb 6, 2025Updated last year
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Scan contig files against PubMLST typing schemes☆297Jun 17, 2026Updated 2 months ago
- "Reads to report" for public health and clinical microbiology☆144Dec 9, 2025Updated 8 months ago
- post processing of bacterial pangenome gene presence/absence matrices☆67Jan 19, 2026Updated 6 months ago
- Create a tree using Mash distances☆189Oct 24, 2023Updated 2 years ago
- Making whole bacterial genome sequencing data analysis easy☆115Apr 22, 2025Updated last year
- Rapid & standardized annotation of bacterial genomes, MAGs & plasmids☆666Aug 7, 2026Updated last week
- Build a partitioned pangenome graph from microbial genomes☆308Updated this week
- Mass screening of contigs for antimicrobial and virulence genes☆507Jul 17, 2026Updated last month
- Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.☆205Jun 10, 2026Updated 2 months ago
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- Antimicrobial Resistance Identification By Assembly☆186Oct 12, 2023Updated 2 years ago
- hybrid assembly pipeline for bacterial genomes☆650Jul 29, 2026Updated 2 weeks ago
- A pipeline for performing genome-wide association tests for bacterial genomes.☆28Apr 11, 2018Updated 8 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…☆157Oct 2, 2025Updated 10 months ago
- Create your own PanViz visualizations☆21Nov 20, 2017Updated 8 years ago
- PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)☆109Jun 2, 2026Updated 2 months ago
- BSR-Based Allele Calling Algorithm☆150Jul 30, 2026Updated 2 weeks ago
- Gene cluster comparison figure generator☆650Dec 22, 2025Updated 7 months ago
- Fast genome and metagenome distance estimation using MinHash☆451Sep 19, 2025Updated 10 months ago
- Deploy open-source AI quickly and easily - Special Bonus Offer • AdRunpod Hub is built for open source. One-click deployment and autoscaling endpoints without provisioning your own infrastructure.
- A tool for generating consensus long-read assemblies for bacterial genomes☆347Jul 24, 2026Updated 3 weeks ago
- 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 8 years ago
- A set of scripts for calculating pairwise SNP distance☆45Feb 19, 2026Updated 5 months ago
- Processing pipeline for pan-genome visulization and exploration☆146Oct 9, 2023Updated 2 years ago
- ☆116Jul 24, 2026Updated 3 weeks ago
- A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences☆67Jul 27, 2026Updated 3 weeks ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆21Feb 15, 2019Updated 7 years ago