wm75/sars-cov-2

Initial analysis of COVID-19 data using Galaxy, BioConda and XSEDE

Dannon Baker, Marius Van Den Beek, John Chilton, Nate Coroar, Delphine LaRiviere, Nicholas Keener, Sergei Kosakovsky, Anton Nekrutenko, James Taylor, Steven Weaver

The is a companion to the manuscript describing the analysis of early COVID-19 data. It contains description of workflows and exact versions of all software used.

It contains the following steps:

1. Pre-processing of raw read data
2. Assembly of COVID-19 genome
3. Estimation of timing for most common recent ancestor (MCRA)
4. Analysis of variation within individual isolates
5. Analysis of Spike protein substitutions
6. Analysis of recombination

The analyses have been performed on Galaxy platform using open source tools from BioConda. All tools were run on XSEDE resources maintained by the Texas Advanced Computing Center (TACC), Pittsburgh Supercomputing Center (PSC), and Indiana University.