Swabs to Genomes: Week 9 (Submit assemblies to NCBI, draft paper)

The blog posts for the previous 8 weeks were written as group assignments by the students taking this “Swabs to Genomes” class.  For the final two weeks of the quarter, I will just briefly describe what we did on those days.

Based on the results from Phylosift, A5-miseq, and RAST we made a call at the end of last week as to which genomes were of sufficiently high quality to upload to NCBI and subsequently publish in a Genome Announcement.  10 genomes met this criteria, 9 of them were various Vibrio species and one was a Shewanella.  On week 9 the students submitted these genomes to NCBI using the WGS Submission Portal.  This took up more than half the time, mostly related to getting the metadata accurate and in the form that NCBI requires.

The homework assignment leading up to week 9 was to draft up a Genome Announcement for their particular bacteria.   So we spent the second half of week 9 class time in groups working on a “consensus” Genome Announcement for each group.   The plan being that the instructors (Ashly Vater and myself) would then write a “consensus consensus” Genome Announcement for discussion on the final day.

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David Coil

David Coil is a Project Scientist in the lab of Jonathan Eisen at UC Davis. David works at the intersection between research, education, and outreach in the areas of the microbiology of the built environment, microbial ecology, and bacterial genomics. Twitter