Segment_liftover : a Python tool to convert segments between genome assemblies.

ABSTRACT: The process of assembling a species' reference genome may be performed in a number of iterations, with subsequent genome assemblies differing in the coordinates of mapped elements. The conversion of genome coordinates between different assemblies is required for many integrative and comparative studies. While currently a number of bioinformatics tools are available to accomplish this task, most of them are tailored towards the conversion of single genome coordinates. When converting the boundary positions of segments spanning larger genome regions, segments may be mapped into smaller sub-segments if the original segment's continuity is disrupted in the target assembly. Such a conversion may lead to a relevant degree of data loss in some circumstances such as copy number variation (CNV) ana

SUBMITTER: Gao B 

PROVIDER: S-EPMC5998006 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature