pha4ge / SARS-CoV-2-Contextual-Data-SpecificationView external linksLinks
Collection template and associated materials for SARS-CoV-2 metadata
☆37Oct 27, 2023Updated 2 years ago
Alternatives and similar repositories for SARS-CoV-2-Contextual-Data-Specification
Users that are interested in SARS-CoV-2-Contextual-Data-Specification are comparing it to the libraries listed below
Sorting:
- ASMNGS20 - 2020 Conference Details☆15Jun 10, 2022Updated 3 years ago
- 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 3 years ago
- ☆20Apr 2, 2025Updated 10 months ago
- Viral (meta)-genome assembly pipeline.☆17Jan 27, 2026Updated 2 weeks ago
- SARs-CoV-2 Primer schemes☆16May 14, 2025Updated 9 months ago
- Small collection of tools for performing quality control on coronavirus sequencing data and genomes☆49Apr 25, 2024Updated last year
- Nextflow workflow template repository☆20Dec 15, 2025Updated last month
- A tool in order to accurately remove primer sequences from NGS reads in an amplicon experiment☆20Nov 12, 2025Updated 3 months ago
- Bioinformatics Pipeline and Visualization resources☆61Aug 30, 2024Updated last year
- The Genomic Epidemiology Application Ontology describes the genomics, laboratory, clinical and epidemiological contextual information req…☆24Updated this week
- Rapid identification of Staphylococcus aureus agr locus type and agr operon variants.☆10Jan 6, 2023Updated 3 years ago
- Code Safety Inspection Service☆20Sep 23, 2022Updated 3 years ago
- Bacterial surveillance pipeline.☆27Dec 30, 2025Updated last month
- A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), wit…☆91Nov 8, 2023Updated 2 years ago
- Validate and submit reads using Webin-CLI in batch.☆11Aug 3, 2023Updated 2 years ago
- interactive barplot for amplicon sequencing☆13Dec 5, 2024Updated last year
- Static website for the PH4AGE alliance☆13Oct 27, 2023Updated 2 years ago
- Nextstrain build for dengue virus☆13Dec 16, 2025Updated last month
- NCBI Pathogen Detection Portal toolkit☆11Sep 6, 2023Updated 2 years ago
- ARTIC SARS-CoV-2 workflow and reporting☆50Apr 25, 2025Updated 9 months ago
- Read contamination removal☆25Jan 24, 2024Updated 2 years ago
- Programmatically interact with the GISAID database.☆80Aug 5, 2025Updated 6 months ago
- app to collapse Pango lineages for reporting☆12Dec 9, 2025Updated 2 months ago
- Renders SVG schema of SARS-CoV-2 clade as defined by Nextstrain☆16Nov 24, 2025Updated 2 months ago
- Depth-weighted De-Mixing☆127Updated this week
- A COVID-19 CoV Genetics (CG) browser to inform therapeutics development☆26Jan 12, 2026Updated last month
- A standardized browser-based spreadsheet editor and validator that can be run offline and locally, and which includes templates for SARS-…☆119Feb 3, 2026Updated last week
- 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 last year
- Documentation for analyzing SARS-Cov2 samples.☆11Jun 4, 2020Updated 5 years ago
- ☆13Aug 20, 2025Updated 5 months ago
- Course materials for an introduction to SARS-CoV-2 sequencing data analysis☆14Aug 15, 2024Updated last year
- Benchmark datasets for WGS analysis of SARS-CoV-2. (https://peerj.com/articles/13821/)☆59Mar 23, 2023Updated 2 years ago
- Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure☆173Nov 27, 2025Updated 2 months ago
- ☆50Mar 11, 2022Updated 3 years ago
- VarSkip multiplex PCR designs for SARS-CoV-2 sequencing☆14Jun 14, 2022Updated 3 years ago
- Reference-based consensus creation☆58Updated this week
- Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens☆37Jan 22, 2026Updated 3 weeks ago
- ☆13Sep 1, 2020Updated 5 years ago
- ☆20Jan 30, 2026Updated 2 weeks ago