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This repo summarises the data sources, web application, tools and reviews paper of SARS-Cov-2. Trace the study progress of SARS-Cov-2 based on GISAID data.

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SARS-Cov-2 data source, methods, publications summary

This repo summarize the tools used in the analysis of SARS-Cov data. Some papers are also recommended here.

Data Sources

1, GISAID: Global Initiative on Sharing All Inflenza Data: https://www.gisaid.org/

The GISAID Initiative promotes the rapid sharing of data from all influenza viruses and the coronavirus causing COVID-19.

2, COG-UK Mutation Explorer: http://sars2.cvr.gla.ac.uk/cog-uk/

This gives the SARS-Cov data in UK, including data update, features analysis(anigenic, drug resistance, et al), and very good visulization.

3, CoV-GLUE: A Web Application for Tracking SARS-CoV-2 Genomic Variation: http://cov-glue.cvr.gla.ac.uk/

CoV-GLUE maintains a database of mutations, insertions and deletions which have been observed in GISAID hCoV-19 sequences sampled from ongoing COVID-19 pandemic.

Genome annotation of SARS-Cov-2 in GFF format. There is a link avaliable for GFF format reference. https://www.ensembl.org/info/website/upload/gff.html

5, CDC(Centers for Disease Control and Prevention) https://github.com/CDCgov

Gives data about prime, sequencing data summary...

ITF_Power_BI : gives a summary for SARS-Cov data.

6, COVID-19 Data Repository by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University https://github.com/CSSEGISandData/COVID-19

very cool real-time dashboad for SARS-Cov. This also gives summary and link of lots of data sources.

7, OWID(our world in data) https://github.com/owid/covid-19-data

a repo collect the published data including SARS-Cov, hospitalization, tests, vaccinations...

phylogenetic trees of fully public SARS-CoV-2 sequences

phylogenetic trees of fully public SARS-CoV-2 sequences updated daily.

SARS-Cov-2 variant mutation tracker

Tools -- focusing on github code based on publications

1, Nextstrain https://github.com/nextstrain and web

Real-time tracking of pathogen evolution. There are many related tools:

Nextclade : Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement

agur : Pipeline components for real-time phylodynamic analysis

There are some data available.

pangolin: Software package for assigning SARS-CoV-2 genome sequences to global lineages.

3, CDC(Centers for Disease Control and Prevention) https://github.com/CDCgov

MIcrobetrace : The Visualization Multitool for Molecular Epidemiology and Bioinformatics

ITF_Power_BI : code for dashboard

4, OWID(our world in data) https://github.com/owid/covid-19-data

This repo collect scripts to generate data like vaccination, hospitail, tests...

Publications

reviews

1, Harvey, William T., et al. "SARS-CoV-2 variants, spike mutations and immune escape." Nature Reviews Microbiology, 2021

This review summarize literatures on mutations of SARS-CoV-2 spike protein, focusing on their impacts on antigenicity. There are also S-protein structrure to explain the mutations causing immune escape.

prediction the next "omicron"

1, Maher M C, Bartha I, Weaver S, et al. Predicting the mutational drivers of future SARS-CoV-2 variants of concern[J]. Science translational medicine, 2022, 14(633): eabk3445.

This paper is to predict which existing amino acid mutations in SARS-CoV-2 might contribute to future variants of concern. code: https://github.com/cyrusmaher/MutationEpiScore

2, Obermeyer F, Jankowiak M, Barkas N, et al. Analysis of 6.4 million SARS-CoV-2 genomes identifies mutations associated with fitness[J]. Science, 2021: abm1208.

developed a model-- PyR0: a hierarchical Bayesian multinomial logistic regression model that infers relative prevalence of all viral lineages across geographic regions, detects lineages increasing in prevalence, and identifies mutations relevant to fitness. PyR0 : https://github.com/broadinstitute/pyro-cov

proteomics

1, Bojkova D, Klann K, Koch B, et al. Proteomics of SARS-CoV-2-infected host cells reveals therapy targets[J]. Nature, 2020, 583(7816): 469-472.

determined the infection profile of SARS-CoV-2 by translatome3 and proteome proteomics at different times after infection.

data: http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD017710

web lineked to the paper http://corona.papers.biochem2.com/

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This repo summarises the data sources, web application, tools and reviews paper of SARS-Cov-2. Trace the study progress of SARS-Cov-2 based on GISAID data.

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