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Nanopore sequencing data analysis: state of the art, applications and challenges

The nanopore sequencing process is based on the transit of a DNA molecule through a nanoscopic pore, and since the 90s is considered as one of the most promising approaches to detect polymeric molecules. In 2014, Oxford Nanopore Technologies (ONT) launched a beta-testing program that supplied the scientific community with the first prototype of a nanopore se- quencer: the MinION. Thanks to this program, several research groups had the opportunity to evaluate the performance of this novel instrument and develop novel computational approaches for analyzing this new generation of data. Despite the short period of time from the release of the MinION, a large number of algorithms and tools have been de- veloped for base calling, data handling, read mapping, de novo assembly and variant discovery. Here, we face the main com- putational challenges related to the analysis of nanopore data, and we carry out a comprehensive and up-to-date survey of the algorithmic solutions adopted by the bioinformatic community comparing performance and reporting limits and advan- tages of using this new generation of sequences for genomic analyses. Our analyses demonstrate that the use of na nopore data dramatically improves the de novo assembly of genomes and allows for the exploration of structural var iants with an unprecedented accuracy and resolut ion. However, despite the impressive improve- ments reached by ONT in the past 2 years, the use of these data fo r small-variant calling is still challenging, and at present, it needs to be coupled with complementary short sequences for mitiga ting the intrinsic biases of nanopore sequencing technology.

Briefings in Bioinformatics, 2017

Autori esterni: Alberto Magi (Universita' di Firenze), Roberto Semeraro (Universita' di Firenze), Alessandra Mingrino (Universita' di Firenze), Betti Giusti (Universita' di Firenze)
Autori IIT:

Tipo: Contributo in rivista ISI
Area di disciplina: Information Technology and Communication Systems

File: Articolo-2017-brief-bioinfo-nanopore-bbx062.pdf

Attività: Biologia computazionale