This repo summarize the tools used in the analysis of SARS-Cov data. Some papers are also recommended here.
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.
4, Nextstrain - ncov https://github.com/nextstrain/ncov/blob/50ceffa/defaults/annotation.gff
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...
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
9，UShER phylogenies of public data http://hgdownload.soe.ucsc.edu/goldenPath/wuhCor1/UShER_SARS-CoV-2/
phylogenetic trees of fully public SARS-CoV-2 sequences updated daily.
10, outbreak.info https://outbreak.info/ Github: https://github.com/outbreak-info/R-outbreak-info
SARS-Cov-2 variant mutation tracker
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
2, CoV-lineages https://github.com/cov-lineages
3, CDC(Centers for Disease Control and Prevention) https://github.com/CDCgov
4, OWID(our world in data) https://github.com/owid/covid-19-data
This repo collect scripts to generate data like vaccination, hospitail, tests...
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.
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
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/