BiG Talks! Petabase-scale sequence alignment catalyzes discovery of novel Coronaviruses
We are excited to welcome Artem Babaian (University of British Columbia, Canada) to speak about Serratus: a project to uncover novel coronavirus genomes from public data.
The SciLifeLab Bioinformatics and Genomics seminar series (“BiG Talks!”) is an initiative that aims to give inspiration to the SciLifeLab community and to create new networking possibilities. The BiG Talks will rotate between different SciLifeLab nodes.
The talk and questions will be live-streamed over YouTube and also projected in SciLifeLab Solna and Uppsala.
The previously announced streaming & fika in SciLifeLab Solna / Uppsala has now been cancelled, due to the worsening Covid-19 situation.
The speaker is interested in having individual conversations with interested parties and potential collaborators. Please let Phil Ewels (firstname.lastname@example.org) if this is of interest to you.
Contact person: Dr. Phil Ewels, NGI SciLifeLab Stockholm.
See also the main SciLifeLab event page for this talk.
Petabase-scale sequence alignment catalyzes discovery of novel Coronaviruses
Public sequence data represents a major opportunity for viral discovery, but its exploration has been inhibited by a lack of efficient methods for searching this corpus, which is currently at the petabase scale and growing exponentially. To address the ongoing pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 and expand the known sequence diversity of viruses, we aligned pangenomes for coronaviruses (CoV) and other viral families to 5.6 petabases of public sequencing data from 3.8 million biologically diverse samples. To implement this strategy, we developed a cloud computing architecture, Serratus, tailored for ultra-high throughput sequence alignment at the petabase scale. From this search, we identified and assembled thousands of CoV and CoV-like genomes and genome fragments ranging from known strains to putatively novel genera. We generalise this strategy to other viral families, identifying several novel deltaviruses and huge bacteriophages. To catalyse a new era of viral discovery we made millions of viral alignments and family identifications freely available to the research community. Expanding the known diversity and zoonotic reservoirs of CoV and other emerging pathogens can accelerate vaccine and therapeutic developments for the current pandemic, and help us anticipate and mitigate future ones.
Artem Babaian has a BSc in Molecular Genetics from McMaster University, Hamilton, ON and PhD in Medical Genetics from the University of British Columbia, Vancouver, BC. His research focuses is on RNA genetics, specifically the genetic and epigenetic variation within human ribosomal RNA and it’s influence on cancer biology. To help the global research effort in the fight against COVID-19, Dr. Babaian initiated and led an international consortium of 13 scientists to develop the Serratus computing architecture, one of the most powerful cloud computing systems ever used in computational biology.