Jointly aligning a group of DNA reads improves accuracy of identifying large deletions - Archive ouverte HAL Access content directly
Journal Articles Nucleic Acids Research Year : 2018

Jointly aligning a group of DNA reads improves accuracy of identifying large deletions

(1) , (1, 2) , (1, 2) , (3)
1
2
3

Abstract

Performing sequence alignment to identify structural variants, such as large deletions, from genome se-quencing data is a fundamental task, but current methods are far from perfect. The current practice is to independently align each DNA read to a reference genome. We show that the propensity of ge-nomic rearrangements to accumulate in repeat-rich regions imposes severe ambiguities in these alignments , and consequently on the variant calls––with current read lengths, this affects more than one third of known large deletions in the C. Venter genome. We present a method to jointly align reads to a genome, whereby alignment ambiguity of one read can be disambiguated by other reads. We show this leads to a significant improvement in the accuracy of identifying large deletions (≥20 bases), while imposing minimal computational overhead and maintaining an overall running time that is at par with current tools. A software implementation is available as an open-source Python program called JRA at https://bitbucket.org/jointreadalignment/jra-src.
Fichier principal
Vignette du fichier
gkx1175.pdf (990.25 Ko) Télécharger le fichier
Origin : Publication funded by an institution
Loading...

Dates and versions

hal-01727521 , version 1 (09-03-2018)

Licence

Attribution - CC BY 4.0

Identifiers

Cite

Anish M S Shrestha, Martin C. Frith, Kiyoshi Asai, Hugues Richard. Jointly aligning a group of DNA reads improves accuracy of identifying large deletions. Nucleic Acids Research, 2018, 46 (3), pp.e18. ⟨10.1093/nar/gkx1175⟩. ⟨hal-01727521⟩
831 View
49 Download

Altmetric

Share

Gmail Facebook Twitter LinkedIn More