Skip to Main content Skip to Navigation
Journal articles

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

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
Document type :
Journal articles
Complete list of metadata

Cited literature [24 references]  Display  Hide  Download
Contributor : Gestionnaire 2 HAL-UPMC Connect in order to contact the contributor
Submitted on : Friday, March 9, 2018 - 11:30:26 AM
Last modification on : Sunday, June 26, 2022 - 9:50:04 AM
Long-term archiving on: : Sunday, June 10, 2018 - 1:49:51 PM


Publication funded by an institution


Distributed under a Creative Commons Attribution 4.0 International License



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, Oxford University Press, 2018, 46 (3), pp.e18. ⟨10.1093/nar/gkx1175⟩. ⟨hal-01727521⟩



Record views


Files downloads