Resources

Resources

This page lists relevant links for the COVID-19 Biohackathon 2020. See https://github.com/virtual-biohackathons/covid-19-bh20 or we are putting the band back together

General

• News category
• Wikipedia/wikidata is tracking the pandemic both internationally and locally
• What does a pandemic mean for the USA and others following the Italian model
• Popular article 'Act today or people will die' on COVID-19 and its spread
• Live maps from Bing
• The Economist has an interesting article on COVID-19 drug development - unfortunately it is paywalled.
• Wikidata: SARS-CoV-2, COVID-19 (and this book with a growing list of queries)
• WikiPathways: https://www.wikipathways.org/index.php/Pathway:WP4846

Pandemic & science

• WHO pandemic phase descriptions and actions
• Fighting COVID-19 with AI: efforts and lessons from China
• COVID-19 resource center from The Lancet
• A human monoclonal antibody blocking SARS-CoV-2 infection PDF

Data resources

• GISAID has the most complete sequence data collection of SARS-CoV-2. But GISAID has lots of restrictions on releasing data.
• NCBI Reference sequence Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome
• NCBI SRA has a growing amount of public raw data for science - but note the usage licenses! We may be able to redistribute with appropriate metadata.
• Other SARS-CoV-2 sequence data from NCBI
• SRP250294 This is a set of Illumina and Oxford Nanopore data depleted of host sequences and other contaminating sequences.
• sequencing data and structures from EMBL-EBI https://www.ebi.ac.uk/ena/pathogens/covid-19

Software resources

• Erik Garrison on assembly of nanopore.

Workflows and pipelines

• Initial analysis of SARS-CoV-2 data using Galaxy and BioConda
• nextstrain phylogeny analysis using data from GISAID
• Artic Nanopore workflow