Dr. Siavash Mirarab
Assistant Professor, UCSD, Dept. of Electrical & Computer Engineering
Faculty Profile
Assembly-free and alignment-free sample identification and phylogenetic placement using genome skims
Thursday, Oct. 24, 2 PM, RRI 101
Abstract: The ability to inexpensively describe taxonomic diversity is critical in this era of rapid climate and biodiversity changes. The recent genome-skimming approach extends current barcoding practices beyond short markers by applying low-pass sequencing and recovering whole organelle genomes computationally. This approach discards the nuclear DNA, which constitutes the vast majority of the data. In contrast, we suggest using all unassembled reads. We introduce an assembly-free and alignment-free tool, Skmer, to compute genomic distances between the query and reference genome skims. Skmer is based on a fast computation of Jaccard index and appropriate corrections for lack of coverage. Skmer shows excellent accuracy in estimating distances and identifying the closest match in reference datasets. When paired with our new phylogenetic placement tool, APPLES, it can perform distance-based phylogenetics.
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