Proof that I did something during my first rotation at UCLA Genetics with the Garud lab!
Overall project theme: How does strain structure in the ocean microbiome compare to the human microbiome?
The TARA project revolves around shotgun sequenced DNA samples collected by the TARA oceans expedition, corresponding to the prokaryotic fraction. Samples were downloaded by SRA accession and processed via the MIDAS pipeline (https://github.com/snayfach/MIDAS) And further data analysis ensues.
The sar86 project revolves around single cell genome isolates of the Sar86 microbe, obtained from PATRIC: https://www.patricbrc.org/view/GenomeList/?keyword(%22sar86%22)#view_tab=genomes&filter=false
Attempts were made to perform a multiple sequence alignment. Many tools were not up to the task.