A pipeline that ingests SARS-CoV-2 (i.e. nCoV) data from GISAID and Genbank, transforms it, stores it on S3, and triggers Nextstrain nCoV rebuilds.
☆37Mar 3, 2026Updated this week
Alternatives and similar repositories for ncov-ingest
Users that are interested in ncov-ingest are comparing it to the libraries listed below
Sorting:
- 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
- Nextstrain build for mpox virus☆50Feb 16, 2026Updated 2 weeks ago
- Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement☆251Feb 27, 2026Updated last week
- Nextstrain build for Zika virus☆10Dec 19, 2025Updated 2 months ago
- Data and scripts for Zika virus tutorial☆10Oct 14, 2025Updated 4 months ago
- Validate and submit reads using Webin-CLI in batch.☆11Aug 3, 2023Updated 2 years ago
- Nextstrain build for dengue virus☆13Dec 16, 2025Updated 2 months ago
- Tools for analyzing and comparing SARS-CoV-2 phylogenies☆10Nov 21, 2020Updated 5 years ago
- Nanopore read de-multiplexer☆13Mar 25, 2020Updated 5 years ago
- A tool for exploring large trees in the browser☆123Feb 4, 2026Updated last month
- Programmatically interact with the GISAID database.☆80Aug 5, 2025Updated 7 months ago
- Genomic Assemblies Merger for NGS☆26Nov 10, 2023Updated 2 years ago
- SARs-CoV-2 Primer schemes☆16May 14, 2025Updated 9 months ago
- High-performance analytical database for sequence alignment data☆18Updated this week
- ☆25Jun 25, 2024Updated last year
- Official place for proposals and details around monkeypox virus lineage designations☆23Dec 9, 2025Updated 2 months ago
- A tool in order to accurately remove primer sequences from NGS reads in an amplicon experiment☆20Nov 12, 2025Updated 3 months ago
- Systematic ProtEin AnnotatoR☆19Sep 20, 2025Updated 5 months ago
- Minhash and maxhash library in Python, combining flexibility, expressivity, and performance.☆22Dec 14, 2024Updated last year
- Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories☆38Feb 20, 2026Updated 2 weeks ago
- ☆12Feb 15, 2023Updated 3 years ago
- python simulation interface for molecular modeling. To cite this software publication: https://www.sciencedirect.com/science/article/pii/…☆13Aug 24, 2016Updated 9 years ago
- Utility to alias and dealias pango lineages☆23Dec 18, 2023Updated 2 years ago
- An open-source software package to power microbial genomic databases☆66Updated this week
- Fast viral consensus genome reconstruction☆26Feb 5, 2026Updated last month
- k-SLAM ultra fast alignment and taxonomic classification of metagenomic datasets☆23Nov 18, 2018Updated 7 years ago
- SARS-CoV-2 genome data analysis☆10Dec 6, 2025Updated 3 months ago
- A utility for splitting mixed origin NGS reads☆10Jun 1, 2021Updated 4 years ago
- Mycobacterium tuberculosis complex lineage typing☆10Jun 22, 2025Updated 8 months ago
- ☆13Nov 26, 2025Updated 3 months ago
- OpenBabel wrapper package for R☆10Feb 17, 2026Updated 2 weeks ago
- Predict prokaryotic hosts for phage (meta) genomic sequences☆11Apr 4, 2022Updated 3 years ago
- Metagenomics Pipeline Repository for January, 2015 NCBI/ADDS Hackathon at NIH☆10Oct 31, 2016Updated 9 years ago
- The data API server for outbreak.info☆11Jan 27, 2025Updated last year
- Bitpacked sequence trait and implementation☆16Feb 27, 2026Updated last week
- NCBI Pathogen Detection Portal toolkit☆11Sep 6, 2023Updated 2 years ago
- Light phylogeny library for Rust☆10Oct 24, 2025Updated 4 months ago
- ☆25Feb 21, 2017Updated 9 years ago
- ARTIC SARS-CoV-2 workflow and reporting☆50Apr 25, 2025Updated 10 months ago