Cluster Investigation & Virus Epidemiology Tool
☆50Jun 17, 2025Updated 10 months ago
Alternatives and similar repositories for civet
Users that are interested in civet are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Local Lineage and Monophyly Assessment☆16Aug 5, 2021Updated 4 years ago
- Systematic ProtEin AnnotatoR☆19Sep 20, 2025Updated 7 months ago
- ☆38Jan 12, 2026Updated 3 months ago
- Molecular Epidemiology of Viruses in R☆20Sep 24, 2015Updated 10 years ago
- A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), wit…☆91Nov 8, 2023Updated 2 years ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- Quasitools is a collection of tools for analysing viral quasispecies data.☆27Nov 25, 2021Updated 4 years ago
- Global phylogenies of SARS-CoV-2 sequences☆85Oct 24, 2023Updated 2 years ago
- Epidemiological modeling framework for pathogen population genetics and evolution.☆18Oct 7, 2024Updated last year
- Phylogenetics between and within hosts at once, all along the genome.☆51Oct 2, 2024Updated last year
- ASMNGS20 - 2020 Conference Details☆15Jun 10, 2022Updated 3 years ago
- ☆30Sep 21, 2023Updated 2 years ago
- Stitch together Nanopore tiled amplicon data without polishing a reference☆17Jan 29, 2024Updated 2 years ago
- Reconstruction of transmission trees using genomic data☆72Sep 27, 2023Updated 2 years ago
- A multi-algorithmic framework for phylogenetic inference☆14Nov 28, 2025Updated 5 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.
- snipit: summarise snps relative to your reference sequence☆172Jan 13, 2026Updated 3 months ago
- The ARTIC fieldbioinformatics pipeline☆131Apr 24, 2026Updated last week
- ☆74Jan 23, 2024Updated 2 years ago
- Report salient qPCR primer/probe or immune epitope mismatches info against a set of pathogen isolate genomes☆16Mar 11, 2025Updated last year
- Predict MLST directly from uncorrected long reads☆27Oct 31, 2025Updated 6 months ago
- Small collection of tools for performing quality control on coronavirus sequencing data and genomes☆49Apr 25, 2024Updated 2 years ago
- rapid serotyping of Vibrio parahaemolyticus from whole genome sequencing data using serogroup-specific genes☆10Sep 2, 2021Updated 4 years ago
- CRAN Task View: Epidemiology☆23Mar 17, 2026Updated last month
- Pipeline to automatically analyse SARS-CoV-2 Whole genome sequencing Illumina data obtained using EasySeq SARS-CoV-2/COVID-19 Whole Geno…☆15Jul 26, 2022Updated 3 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.
- Process consensus file for COG-UK data☆13Sep 7, 2021Updated 4 years ago
- A snakemake-based pipeline for assembling and polishing long genomes from long nanopore reads☆68Nov 4, 2021Updated 4 years ago
- Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement☆253Apr 25, 2026Updated last week
- ☆21Jan 23, 2026Updated 3 months ago
- Ultrafast Sample Placement on Existing Trees☆140Feb 6, 2026Updated 2 months ago
- Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction☆251Apr 24, 2026Updated last week
- Resources for calling and describing the circulating lineages of SARS-CoV-2☆38Apr 6, 2021Updated 5 years ago
- MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumin…☆47Sep 8, 2025Updated 7 months ago
- Bayesian inference of ancestral dates on bacterial phylogenetic trees☆98Dec 9, 2025Updated 4 months ago
- Serverless GPU API endpoints on Runpod - Get Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- Viral Annotation DefineR: classification and annotation of viral sequences based on RefSeq annotation☆114Mar 5, 2026Updated last month
- A package for designing activity-informed nucleic acid diagnostics for viruses.☆35Feb 14, 2023Updated 3 years ago
- A collection of sequencing protocols and bioinformatic resources for SARS-CoV-2 sequencing.☆347Apr 12, 2023Updated 3 years ago
- Archived - please see updated sccmec tool at link below☆13Aug 30, 2024Updated last year
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆29Jul 18, 2025Updated 9 months ago
- Nanopore read de-multiplexer☆13Mar 25, 2020Updated 6 years ago
- C++ tools for NCBI taxonomy tasks☆12Jun 26, 2025Updated 10 months ago