https://github.com/nextstrain/ncov
Nextstrain build for novel coronavirus SARS-CoV-2
https://github.com/nextstrain/ncov
ncov nextstrain pathogen sars-cov-2
Last synced: 23 days ago
JSON representation
Nextstrain build for novel coronavirus SARS-CoV-2
- Host: GitHub
- URL: https://github.com/nextstrain/ncov
- Owner: nextstrain
- License: mit
- Created: 2020-01-19T17:23:17.000Z (over 5 years ago)
- Default Branch: master
- Last Pushed: 2024-10-23T22:34:28.000Z (6 months ago)
- Last Synced: 2024-10-24T11:41:43.128Z (6 months ago)
- Topics: ncov, nextstrain, pathogen, sars-cov-2
- Language: Python
- Homepage: https://nextstrain.org/ncov
- Size: 28.1 MB
- Stars: 1,353
- Watchers: 77
- Forks: 403
- Open Issues: 94
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
- awesome-starred - nextstrain/ncov - Nextstrain build for novel coronavirus SARS-CoV-2 (others)
README
[](https://github.com/nextstrain/ncov/releases)
[](https://docs.nextstrain.org/projects/ncov/en/latest/reference/change_log.html)
# About
This repository analyzes viral genomes using [Nextstrain](https://nextstrain.org) to understand how SARS-CoV-2, the virus that is responsible for the COVID-19 pandemic, evolves and spreads.
We maintain a number of publicly-available builds, visible at [nextstrain.org/ncov](https://nextstrain.org/ncov).
[See our change log for details about backwards-incompatible or breaking changes to the workflow](https://docs.nextstrain.org/projects/ncov/en/latest/reference/change_log.html).
Visit [the workflow documentation](https://docs.nextstrain.org/projects/ncov) for tutorials and reference material.
## Download formatted datasets
The hCoV-19 / SARS-CoV-2 genomes were generously shared via GISAID. We gratefully acknowledge the Authors, Originating and Submitting laboratories of the genetic sequence and metadata made available through GISAID on which this research is based.
In order to download the GISAID data to run the analysis yourself, please see [this guide](https://docs.nextstrain.org/projects/ncov/en/latest/analysis/data-prep.html).
> Please note that `data/metadata.tsv` is no longer included as part of this repo. However, we provide continually-updated, pre-formatted metadata & fasta files for download through GISAID.
## Read previous Situation Reports
We issued weekly Situation Reports for the first ~5 months of the pandemic. You can find the Reports and their translations [here](https://nextstrain.org/ncov-sit-reps).
## FAQs
- Can't find your sequences in Nextstrain? Check [here](./docs/data_faq.md) for common reasons why your sequences may not be appearing.
You can also use [clades.nextstrain.org](https://clades.nextstrain.org/) to perform some basic quality control on your sequences. If they are flagged by this tool, they will likely be excluded by our pipeline.
- For information about how clades are defined, and the currently named clades, please see [here](./docs/naming_clades.md). To assign clades to your own sequences, you can use our clade assignment tool at [clades.nextstrain.org](https://clades.nextstrain.org/).
## Bioinformatics notes
Site numbering and genome structure uses [Wuhan-Hu-1/2019](https://www.ncbi.nlm.nih.gov/nuccore/MN908947) as reference. The phylogeny is rooted relative to early samples from Wuhan. Temporal resolution assumes a nucleotide substitution rate of [8 × 10^-4 subs per site per year](http://virological.org/t/phylodynamic-analysis-176-genomes-6-mar-2020/356). There were SNPs present in the nCoV samples in the first and last few bases of the alignment that were masked as likely sequencing artifacts.
# Contributing
We welcome contributions from the community! Please note that we strictly adhere to the [Contributor Covenant Code of Conduct](https://github.com/nextstrain/.github/blob/master/CODE_OF_CONDUCT.md).
### Contributing to software or documentation
Please see our [Contributor Guide](https://github.com/nextstrain/.github/blob/master/CONTRIBUTING.md) to get started!
### Contributing data
**Please note that we automatically pick up any SARS-CoV-2 data that is submitted to GISAID.**
If you're a lab and you'd like to get started sequencing, please see:
* [Protocols from the ARTIC network](https://www.protocols.io/groups/artic/publications)
* [Funding opportunities for sequencing efforts](https://twitter.com/firefoxx66/status/1242147905768751106)
* Or, if these don't meet your needs, [get in touch](mailto:[email protected])
---
# Get in touch
To report a bug, error, or feature request, please [open an issue](https://github.com/nextstrain/ncov/issues).
For questions, head over to the [discussion board](https://discussion.nextstrain.org/); we're happy to help!