Open Peer Review Discuss this article (0) Comments SOFTWARE TOOL ARTICLE segment_liftover : a Python tool to convert segments between genome assemblies [version 1; referees: 1 approved, 1 approved with reservations] Bo Gao , Qingyao Huang , Michael Baudis 1,2 Institute of molecular Life Sciences, University of Zürich, Zürich, CH-8057, Switzerland Swiss Institute of Bioinformatics, University of Zürich, Zürich, CH-8057, Switzerland 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) analysis, where the quantitative representation of a genomic region takes precedence over base-specific accuracy. aims at continuity-preserving segment_liftover remapping of genome segments between assemblies and provides features such as approximate locus conversion, automated batch processing and comprehensive logging to facilitate processing of datasets containing large numbers of structural genome variation data. Keywords Genome assembly, liftover, remap, copy number segment. This article is included in the Python Collection collection. 1,2 1,2 1,2 1 2 Referee Status: Invited Referees version 2 published 08 Jun 2018 version 1 published 14 Mar 2018 1 2 report report report , Netherlands Oscar Krijgsman Cancer Institute, Netherlands 1 , National Institutes of Ryan K. Dale Health, USA 2 14 Mar 2018, :319 (doi: ) First published: 7 10.12688/f1000research.14148.1 08 Jun 2018, :319 (doi: ) Latest published: 7 10.12688/f1000research.14148.2 v1 Page 1 of 13 F1000Research 2018, 7:319 Last updated: 26 JUN 2018