Novel read density distribution score shows possible aligner artefacts, when mapping a single chromosome
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Abnizova, I. (2018). Novel read density distribution score shows possible aligner artefacts, when mapping a single chromosome. BMC Genomics, 19 (Suppl 3. 92)https://doi.org/10.1186/s12864-018-4475-6
The use of artificial data to evaluate the performance of aligners and peak callers not only improves its accuracy and reliability, but also makes it possible to reduce the computational time. One of the natural ways to achieve such time reduction is by mapping a single chromosome. We investigated whether a single chromosome mapping causes any artefacts in the alignments’ performances. In this paper, we compared the accuracy of the performance of seven aligners on well-controlled simulated benchmark data which was sampled from a single chromosome and also from a whole genome. We found that commonly used statistical methods are insufficient to evaluate an aligner performance, and applied a novel measure of a read density distribution similarity, which allowed to reveal artefacts in aligners’ performances.
The computer code development and biodiversity research were supported by the Ministry of Education and Science of the Russian Federation grant #14.W03.31.0015. The algorithm development was supported by ICG SB RAS budget project 0324–2018-0017. The software testing on supercomputer cluster was supported by the Russian Science Foundation (grant no. 16–14-10216). The publication costs for this article were funded by RSF (grant no. 16–14-10216).
External DOI: https://doi.org/10.1186/s12864-018-4475-6
This record's URL: https://www.repository.cam.ac.uk/handle/1810/294506
Attribution 4.0 International
Licence URL: https://creativecommons.org/licenses/by/4.0/