Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health concern.
☆69Oct 1, 2026Updated this week
Alternatives and similar repositories for public_health_bioinformatics
Users that are interested in public_health_bioinformatics are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, es…☆42Aug 5, 2024Updated 2 years ago
- ☆28Aug 2, 2023Updated 3 years ago
- UPHL's Reference Free Pipeline☆29Sep 4, 2026Updated 3 weeks ago
- A Nextflow pipeline for viral genomics (Influenza/RSV) supporting Illumina and Nanopore sequencing of clinical and wastewater samples.☆10Jun 9, 2026Updated 3 months ago
- Bacterial surveillance pipeline.☆30Updated this week
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- 🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission☆29Sep 25, 2026Updated last week
- MycoSNP: Whole Genome Sequencing Analysis of Fungal Isolates☆96Jul 23, 2026Updated 2 months ago
- Assign genotypes to Salmonella Paratyphi A isolates using their whole-genome data.☆10Mar 6, 2025Updated last year
- Viral (meta)-genome assembly pipeline.☆23Sep 8, 2026Updated 3 weeks ago
- Assembly of Nanopore Sequencing☆17Sep 1, 2026Updated last month
- 🔥🐦🔥PHoeNIx: a platform agnostic pipeline for healthcare-associated and antimicrobial resistant pathogens☆112Updated this week
- Dockerfiles and documentation on tools for public health bioinformatics☆226Updated this week
- emm Automatic Isolate Labeller☆16Mar 25, 2025Updated last year
- Scripts and reference files to type Group A Streptococcus☆11Aug 31, 2026Updated last month
- 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.
- Reference-based consensus creation☆61Updated this week
- Repo for PrimerSchemes☆20Sep 14, 2026Updated 2 weeks ago
- Ampseer examines reads in fastq format and identifies which multiplex PCR primer set was used to generate the SARS-CoV-2 sequencing libra…☆15Feb 27, 2024Updated 2 years ago
- Bioinformatics Pipeline and Visualization resources☆68Aug 30, 2024Updated 2 years ago
- Depth-weighted De-Mixing☆134Updated this week
- Software for the Tree-Based Scan Statistic☆17Updated this week
- Datasets for https://github.com/nextstrain/nextclade☆47Updated this week
- ☆24Jul 25, 2026Updated 2 months ago
- TaxTriage is a Nextflow workflow designed to agnostically identify and give confidences of microbial organisms within short- or long-read…☆82Updated this week
- 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.
- ☆29May 19, 2026Updated 4 months ago
- ☆22Jun 1, 2026Updated 4 months ago
- Bioinformatics pipeline for SARS-CoV-2 sequencing at CZ Biohub☆25Mar 26, 2022Updated 4 years ago
- viral-ngs: complete pipelines☆75Updated this week
- Benchmark datasets for WGS analysis of SARS-CoV-2. (https://peerj.com/articles/13821/)☆62Mar 23, 2023Updated 3 years ago
- Influenza genome analysis Nextflow workflow☆28Jun 3, 2026Updated 4 months ago
- Quasitools is a collection of tools for analysing viral quasispecies data.☆27Nov 25, 2021Updated 4 years ago
- tool to determine optimal refrerence genome given a set of fasta files☆15May 18, 2023Updated 3 years ago
- A tool easily taken advantage of for in silico serogrouping of Pseudomonas aeruginosa isolates☆15Aug 26, 2024Updated 2 years ago
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- Standard database for the TBProfiler tool☆31Jun 23, 2026Updated 3 months ago
- A Python package to update the MLST database for the mlst tool.☆33Jul 22, 2026Updated 2 months ago
- An SRA tool that takes as input local fastq file from a clinical infection sample, identifies and removes any significant human read, and…☆57Jul 24, 2025Updated last year
- NCBI Pathogen Detection Portal toolkit☆11Sep 6, 2023Updated 3 years ago
- ☆21Apr 2, 2025Updated last year
- The Visualization Multitool for Molecular Epidemiology and Bioinformatics☆104Updated this week
- A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification.☆36Aug 11, 2026Updated last month