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. 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.
Highlights
The first draft version of human genome was published in 20011
The UCSC liftOver tool exists in two flavours, both as web service and command line utility
In research such as analysis of copy number variation (CNV) data, where the quantitative representation of a genomic range takes precedence over base-specific representation, the integrity of a continuous segment indicates the proper conversion between assemblies, but may not be a direct outcome of current re-mapping approaches
Summary
The first draft version of human genome was published in 20011. In subsequent years, several new editions were released to perfect the quality of the genome assembly. This method could provide the best result but is very time-consuming, and is not possible if the original sequence data is not available or does not consist of direct sequences (i.e. segmentation of array based data) Another approach is to convert the coordinates of genome data between assemblies by using a mapping file. The UCSC liftOver tool exists in two flavours, both as web service and command line utility It offers the most comprehensive selection of assemblies for different organisms with the capability to convert between many of them. Remap keeps the integrity of the segment and maps the span to the target assembly In research such as analysis of copy number variation (CNV) data, where the quantitative representation of a genomic range takes precedence over base-specific representation, the integrity of a continuous segment indicates the proper conversion between assemblies, but may not be a direct outcome of current re-mapping approaches. It features two major functional additions over existing tools: First, re-conversion by locus approximation, in instances where a precise conversion of genomic positions fails; and second, the capability to handle any number of files and optional integration into data processing pipelines with supporting features such as automatic file traversal, interruption resumption and detailed logging
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