Accelerating SARS-CoV-2 Low Frequent Variant Calling on Ultra Deep Sequencing Datasets

Abstract

With recent advances in sequencing technology it has become affordable and practical to sequence genomes to very high depth-of-coverage, allowing researchers to discover lowfrequency variants in the genome. However, due to the errors in sequencing it is an active area of research to develop algorithms that can separate noise from the true variants. LoFreq is a state of the art algorithm for low-frequency variant detection but has a relatively long runtime compared to other tools. In addition to this, the interface for running in parallel could be simplified, allowing for multithreading as well as distributing jobs to a cluster. In this work we describe some specific contributions to LoFreq that remedy these issues.

Bryce Kille

PhD student

Bryce (4th year PhD student) received his MS in Bioinformatics and BS in Computer Science + Chemistry from the University of Illinois at Urbana-Champaign. As an undergraduate, he worked at Dow Agrosciences in both the computational biology and cheminformatics groups. His projects included developing software for phylogeny analysis and creating models for compound activity prediction. During his Master’s program, Bryce worked in a biochemistry lab developing software for genome mining as well as a on research project for creating bit-wise algorithms for the C++ STL. One of his main interests is casting biological and chemical problems into theoretical computer science questions.