LRphase: an efficient method for assigning haplotype identity to long reads

Motivation Understanding the functional effects of sequence variation is among the primary goals of contemporary genomics. Individual human genomes contain millions of variants which are thought to contribute to phenotypic variability and differential disease risks at the population level. However, because variants rarely act in isolation, we cannot accurately predict functional effects without first considering the potential effects of other interacting variants on the same chromosome. This information can be obtained by phasing the read data from sequencing experiments. However, no standalone tools are available to simply phase reads based on known haplotypes. Here we present LRphase: a user-friendly utility for simple phasing of long sequencing reads. Availability and Implementation LRphase is implemented in Python, and is freely available at https://github.com/Boyle-Lab/LRphase , under the MIT license. Version 1.1.0, described in this manuscript, is available through the pip and Bioconda repositories (e.g., “pip install lrphase==1.1.0”). Contact [email protected] Supplementary Information Supplementary methods are available as part of the online version of this publication.