Remarkably, three more months have gone by since my last post. We have crowned a new Ph.D. from the lab, Dr. Nigel Delaney, back on 30 October. He gave a fantastic presentation concentrating on his new work estimating the distribution of fitness effects of successful mutations for one of our strains of Methylobacterium. He has now gotten started at his new position at the Broad Institute working with Vamsi Mootha
We’ve also seen two new papers come out, both including Nigel, in fact. The first of these describes ‘Clarity‘, an open-source program to manage lab automation that he worked on with Jose Rojas Echenique. We’ve used this to run our automated, robotic growth analysis system, but it could be applied to any given automation challenge.
Second, we have published a paper describing ‘FREQ-Seq’, a new method to rapidly determine allele frequencies directly from mixed populations. Developed by Lon Chubiz and Miki Lee, this is an efficient way to barcode samples and shine the light of Illumina sequencing on just known sites of interest, thereby generating phenomenal depth of coverage (~150,000x for 100 samples in 3% of a lane) and avoiding any typical Illumina library prep. The bridging primers with barcodes for this can be regenerated from a panel of plasmids available through the non-profit plasmid distribution organization, Addgene.org. Nigel developed a software program, ‘FREQout‘, that allows users to rapidly extract frequency information from the Illumina data. We sent this to Yousif Shamoo’s lab for testing and they’ve completed all the data they needed for part of their paper in press at PNAS in the very first go.