Genome Intelligence

One of the main sequence analysis tasks we want to perform on the UEGP dataset is the evaluation of antibiotic resistance potential in the wastewater microbial community. We have examples of analytical approaches to this problem in several prior studies. A very straightforward approach would be to use the CARD database and associated RGI tools to identify components of the “resistome”. However, RGI works on translated protein sequences, ignoring very short sequences, is optimized for genomes and genomic contigs, and has a 20MB…

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This summer, my students and I are working through analysis of wastewater microbiome sequencing data. The analysis includes 3 timepoints, 11 sampling points, 2 wastewater treatment streams, and 3 replicates of each sample. 198 samples in total. For each sample we have 16S ribosomal and whole genome metagenome sequence data, and mass spec analysis for 10 different antibiotics of interest. Samples were collected by students in areas made accessible to us by Charlotte Water, and sequenced at DHMRI. We need to do several different types…

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