Swabs to Genomes: Week 10 (Review paper, debrief, cost analysis)

Week 10 was the last week of class (that’s a quarter system for all semester-types out there).  In the previous class the students got together in groups and produced “consensus” genome announcements for their groups.   In the intervening week, Ashley and I produced a “consensus consensus” Genome Announcement, taking pieces from the various groups.    Then …

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 …

Swabs to Genomes: Week 8 (Genome Annotation and pathways)

(this blog post was written by group #4 as a writing assignment) Our goal for this week’s lesson was to double check that the genome we sequenced is, in fact, the organism we are interested in. After uploading our sequences up to RAST last week, we found out the results and were able to look …

Swabs to Genomes: Week 7 (Validate Assemblies, Upload to RAST)

(this blog post was written by group #3 as a writing assignment) Last week in class we were introduced to genome assembly and validation by using an open-source bacterial genome assembly program A5-miseq. This program produces high quality genome assemblies by automating processes such data processing, error correction, contig and scaffold assembly, and final verification. …

Swabs to Genomes: Week 6 (Discuss Library Prep)

(This post was written by group #2 as a writing assignment) Since we were about half way through this quarter, the activity we did this past week was to summarize all the experiments we have performed so far, list the consumable materials that were used, and any questions or concerns that may have arisen during …

Swabs to Genomes: Week 4 (Sanger sequences and BLAST)

(this post was written by group #4 as a writing assignment) With a minor setback from last week’s inability to efficiently wash and quantify the amplified DNA, we came back this week with a stronger mindset to pick ourselves back up and turn our failures into a positive. At the start of this week’s class, …

Swabs to Genomes Class: Week 2 (DNA Extractions)

(this post was written by group #2 as a writing assignment) The goal of this week experiment was to extract genomic DNA from our samples for sequencing. Ultimately, we want to characterize the DNA from samples by sequencing them. However, since our isolates are in small amounts, we need to do an additional step (in …