ARTICnetwork & CLIMB-BIG-DATA present a panel discussion on overcoming barriers to SARS-CoV-2 data analysis with Nick Loman and Will Rowe from the University of Birmingham, Áine O'Toole from the University of Edinburgh, Andrew Page from the Quadram Institute and Anna Price from MRC CLIMB and Cardiff University. This was part of a workshop on COVID-19 data analysis.
Topics covered:
Collecting sample metadata
intrapatient variability
Building bridges with policy makers to start sequencing
Data sharing
Improving bioinformatics skills
Pipeline and software validation
Bioinformatics reproducibility and quality
Papers:
The PHA4GE SARS-CoV-2 Contextual Data Specification for Open Genomic Epidemiology https://www.preprints.org/manuscript/202008.0220/v1
MAJORA: Continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance https://www.biorxiv.org/content/10.1101/2020.10.06.328328v1
Genomic sequencing of SARS-CoV-2: a guide to implementation for maximum impact on public health https://www.who.int/publications/i/item/9789240018440
Resources:
https://www.climb.ac.uk/artic-and-climb-big-data-joint-workshop/
https://github.com/SamStudio8/majora
https://soundcloud.com/microbinfie/majora
https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-Specification
https://pha4ge.org/
Software:
https://github.com/cov-lineages/pangolin
https://github.com/artic-network/civet
https://github.com/COG-UK/grapevine
https://github.com/cov-lineages/pangoLEARN
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