segment_liftover : a Python tool to convert segments between genome assemblies [version 2; referees: 2 approved]
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 stud...
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| Format: | Article |
| Language: | English |
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F1000 Research Ltd
2018-06-01
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| Series: | F1000Research |
| Online Access: | https://f1000research.com/articles/7-319/v2 |
| _version_ | 1818872767012929536 |
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| author | Bo Gao Qingyao Huang Michael Baudis |
| author_facet | Bo Gao Qingyao Huang Michael Baudis |
| author_sort | Bo Gao |
| collection | DOAJ |
| description | 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. 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. |
| first_indexed | 2024-12-19T12:44:02Z |
| format | Article |
| id | doaj.art-e5de365d64b6430e998dcd8b8f99f61e |
| institution | Directory Open Access Journal |
| issn | 2046-1402 |
| language | English |
| last_indexed | 2024-12-19T12:44:02Z |
| publishDate | 2018-06-01 |
| publisher | F1000 Research Ltd |
| record_format | Article |
| series | F1000Research |
| spelling | doaj.art-e5de365d64b6430e998dcd8b8f99f61e2022-12-21T20:20:50ZengF1000 Research LtdF1000Research2046-14022018-06-01710.12688/f1000research.14148.216527segment_liftover : a Python tool to convert segments between genome assemblies [version 2; referees: 2 approved]Bo Gao0Qingyao Huang1Michael Baudis2Institute of molecular Life Sciences, University of Zürich, Zürich, CH-8057, SwitzerlandInstitute of molecular Life Sciences, University of Zürich, Zürich, CH-8057, SwitzerlandInstitute of molecular Life Sciences, University of Zürich, Zürich, CH-8057, SwitzerlandThe 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. 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.https://f1000research.com/articles/7-319/v2 |
| spellingShingle | Bo Gao Qingyao Huang Michael Baudis segment_liftover : a Python tool to convert segments between genome assemblies [version 2; referees: 2 approved] F1000Research |
| title | segment_liftover : a Python tool to convert segments between genome assemblies [version 2; referees: 2 approved] |
| title_full | segment_liftover : a Python tool to convert segments between genome assemblies [version 2; referees: 2 approved] |
| title_fullStr | segment_liftover : a Python tool to convert segments between genome assemblies [version 2; referees: 2 approved] |
| title_full_unstemmed | segment_liftover : a Python tool to convert segments between genome assemblies [version 2; referees: 2 approved] |
| title_short | segment_liftover : a Python tool to convert segments between genome assemblies [version 2; referees: 2 approved] |
| title_sort | segment liftover a python tool to convert segments between genome assemblies version 2 referees 2 approved |
| url | https://f1000research.com/articles/7-319/v2 |
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