Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, especially SARS-CoV-2
☆42Aug 5, 2024Updated last year
Alternatives and similar repositories for public_health_viral_genomics
Users that are interested in public_health_viral_genomics are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- ☆27Aug 2, 2023Updated 2 years ago
- Bioinformatics Pipeline and Visualization resources☆65Aug 30, 2024Updated last year
- UPHL's Reference Free Pipeline☆28Updated this week
- CFSAN Shigella Typing Pipeline☆15Jul 6, 2023Updated 2 years ago
- Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories☆39Feb 20, 2026Updated 2 months ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- Static website for the PH4AGE alliance☆13Oct 27, 2023Updated 2 years ago
- Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health con…☆62May 1, 2026Updated last week
- Reference-based consensus creation☆61Updated this week
- Output FASTQ summary statistics in JSON format☆29Oct 30, 2022Updated 3 years ago
- A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification.☆35Dec 2, 2024Updated last year
- Private, browser-based placement of genome sequences on phylogenetic trees using UShER.☆11Nov 22, 2024Updated last year
- MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets☆33Jul 2, 2024Updated last year
- 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
- viral-ngs: complete pipelines☆74Apr 9, 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.
- Prepares a SARS-CoV-2 submission for GISAID, NCBI or ENA. Can read GISAID or NCBI files, or plain fasta+tsv/csv/xls. Finds files in input…☆36May 1, 2022Updated 4 years ago
- Bioinformatics pipeline for SARS-CoV-2 sequencing at CZ Biohub☆25Mar 26, 2022Updated 4 years ago
- Read contamination removal☆25Jan 24, 2024Updated 2 years ago
- A Nextflow pipeline for viral genomics (Influenza/RSV) supporting Illumina and Nanopore sequencing of clinical and wastewater samples.☆10Feb 27, 2026Updated 2 months ago
- VIGOR4☆22Aug 15, 2025Updated 8 months ago
- SARS-CoV-2: detecting recombinations in viruses using large data sets with high sequence similarity☆13Aug 14, 2023Updated 2 years ago
- Influenza data pipeline to automate genotyping assignment☆41Mar 19, 2026Updated last month
- hAMRoaster is an analysis pipeline that can compare the output of tools for detecting AMR genes and provide metrics of their performance☆22Mar 8, 2024Updated 2 years ago
- Bacterial surveillance pipeline.☆27Apr 28, 2026Updated last week
- Proton VPN Special Offer - Get 70% off • AdSpecial partner offer. Trusted by over 100 million users worldwide. Tested, Approved and Recommended by Experts.
- TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomi…☆70Apr 28, 2026Updated last week
- Analysis of the population diversity of SARS-CoV-2 within and between individual patients☆15Apr 30, 2020Updated 6 years ago
- Assembly of Nanopore Sequencing☆17Apr 14, 2026Updated 3 weeks ago
- Benchmark datasets for WGS analysis of SARS-CoV-2. (https://peerj.com/articles/13821/)☆60Mar 23, 2023Updated 3 years ago
- A tool easily taken advantage of for in silico serogrouping of Pseudomonas aeruginosa isolates☆14Aug 26, 2024Updated last year
- Dockerfiles and documentation on tools for public health bioinformatics☆222Updated this week
- SARS-CoV-2 workflow for nanopore sequence data☆42Apr 15, 2026Updated 3 weeks ago
- In silico serotyping, finetyping and Bexsero antigen sequence typing of Neisseria meningitidis☆15Feb 19, 2026Updated 2 months ago
- whole genome MLST analysis☆51Mar 27, 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.
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆29Jul 18, 2025Updated 9 months ago
- INSaFLU-TELEVIR: an free web-based (but also locally installable) bioinformatics suite for virus metagenomic detection and routine genomi…☆41Feb 26, 2026Updated 2 months ago
- LYVE-SET, a method of using hqSNPs to create a phylogeny, especially for outbreak investigations☆26Aug 26, 2024Updated last year
- Nextflow workflows to assign Salmonella serotype based on Genome similarity using MASH, SOURMASH and KMA.☆13Updated this week
- rapid serotyping of Vibrio parahaemolyticus from whole genome sequencing data using serogroup-specific genes☆10Sep 2, 2021Updated 4 years ago
- Influenza genome analysis Nextflow workflow☆26Mar 24, 2026Updated last month
- Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data☆14Jun 12, 2024Updated last year