Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
☆221Aug 27, 2025Updated 11 months ago
Alternatives and similar repositories for gubbins
Users that are interested in gubbins 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 haploid variant calling and core genome alignment☆595Dec 12, 2025Updated 8 months ago
- ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes☆127Jun 2, 2026Updated 2 months ago
- Pan-genome wide association studies☆223May 29, 2024Updated 2 years ago
- Scan contig files against PubMLST typing schemes☆297Jun 17, 2026Updated 2 months ago
- an interactive viewer for populations of bacterial genomes linked by a phylogeny☆133Feb 26, 2024Updated 2 years ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- ⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads☆264Jun 11, 2026Updated 2 months ago
- PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)☆109Jun 2, 2026Updated 2 months ago
- AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and p…☆383Aug 10, 2026Updated last week
- Mass screening of contigs for antimicrobial and virulence genes☆507Jul 17, 2026Updated last month
- Rapid large-scale prokaryote pan genome analysis☆380Nov 3, 2025Updated 9 months ago
- Pairwise SNP distance matrix from a FASTA sequence alignment☆156Dec 31, 2025Updated 7 months ago
- Reorients assembled microbial sequences☆143Jun 30, 2026Updated last month
- Assemble bacterial isolate genomes from Nanopore reads☆136Jan 22, 2025Updated last year
- An updated pipeline for pangenome investigation☆370Jul 2, 2026Updated last month
- 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.
- Rapid & standardized annotation of bacterial genomes, MAGs & plasmids☆666Aug 7, 2026Updated last week
- CFSAN Shigella Typing Pipeline☆15Jun 11, 2026Updated 2 months 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
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆30Jul 18, 2025Updated last year
- SEER, reimplemented in python 🐍🔮☆137Jul 23, 2026Updated 3 weeks ago
- Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.☆154Jul 24, 2026Updated 3 weeks ago
- A tool for generating consensus long-read assemblies for bacterial genomes☆347Jul 24, 2026Updated 3 weeks ago
- Antimicrobial Resistance Identification By Assembly☆186Oct 12, 2023Updated 2 years ago
- hybrid assembly pipeline for bacterial genomes☆650Jul 29, 2026Updated 2 weeks 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.
- Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction☆253Updated this week
- BSR-Based Allele Calling Algorithm☆150Jul 30, 2026Updated 2 weeks ago
- Create a tree using Mash distances☆189Oct 24, 2023Updated 2 years ago
- The tool for in silico serotyping☆65Aug 9, 2026Updated last week
- Circular bacterial genome plots based on BLAST or NUCMER/PROMER alignments☆109Dec 11, 2023Updated 2 years ago
- "Reads to report" for public health and clinical microbiology☆144Dec 9, 2025Updated 8 months ago
- Bayesian inference of ancestral dates on bacterial phylogenetic trees☆99Dec 9, 2025Updated 8 months ago
- Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.☆205Jun 10, 2026Updated 2 months ago
- MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies☆182Apr 16, 2025Updated last year
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Finds SNP sites from a multi-FASTA alignment file☆278Dec 16, 2020Updated 5 years ago
- A python pipeline to identify IS (Insertion Sequence) elements in genome and metagenome☆116Dec 5, 2025Updated 8 months ago
- Build a partitioned pangenome graph from microbial genomes☆308Updated this week
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆27Aug 8, 2022Updated 4 years ago
- Interactive, web tool for exploring pan-genome of bacterial strains☆50Jan 14, 2026Updated 7 months ago
- Split Kmer Analysis☆67May 26, 2022Updated 4 years ago
- A flexible pipeline for complete analysis of bacterial genomes☆522Aug 5, 2026Updated last week