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segment_liftover: a Python tool to convert segments between genome assemblies

View ORCID ProfileBo Gao, View ORCID ProfileQingyao Huang, View ORCID ProfileMichael Baudis
doi: https://doi.org/10.1101/274084
Bo Gao
1University of Zurich, Institute of molecular Life Sciences and Swiss Institute of Bioinformatics, Winterthurerstr. 190, CH-8057 Zürich, Switzerland
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Qingyao Huang
1University of Zurich, Institute of molecular Life Sciences and Swiss Institute of Bioinformatics, Winterthurerstr. 190, CH-8057 Zürich, Switzerland
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Michael Baudis
1University of Zurich, Institute of molecular Life Sciences and Swiss Institute of Bioinformatics, Winterthurerstr. 190, CH-8057 Zürich, Switzerland
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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 subsegments 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. segment_liftover aims at continuity-preserving 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.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted March 01, 2018.
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segment_liftover: a Python tool to convert segments between genome assemblies
Bo Gao, Qingyao Huang, Michael Baudis
bioRxiv 274084; doi: https://doi.org/10.1101/274084
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segment_liftover: a Python tool to convert segments between genome assemblies
Bo Gao, Qingyao Huang, Michael Baudis
bioRxiv 274084; doi: https://doi.org/10.1101/274084

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