Reference-free phylogeny from sequencing data

Abstract

Motivation: Clustering of genetic sequences is one of the key parts of bioinformatics analyses. Resulting phylogenetic trees are beneficial for solving many research questions, including tracing the history of species, studying migration in the past, or tracing a source of a virus outbreak. At the same time, biologists provide more data in the raw form of reads or only on contig-level assembly. Therefore, tools that are able to process those data without supervision need to be developed. Results: In this paper, we present a tool for reference-free phylogeny capable of handling data where no mature-level assembly is available. The tool allows distance calculation for raw reads, contigs, and the combination of the latter. The tool provides an estimation of the Levenshtein distance between the sequences, which in turn estimates the number of mutations between the organisms. Compared to the previous research, the novelty of the method lies in a newly proposed combination of the read and contig measures, a new method for read-contig mapping, and an efficient embedding of contigs.