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- Title
Nano-GLADIATOR: real-time detection of copy number alterations from nanopore sequencing data.
- Authors
Magi, Alberto; Bolognini, Davide; Bartalucci, Niccoló; Mingrino, Alessandra; Semeraro, Roberto; Giovannini, Luna; Bonifacio, Stefania; Parrini, Daniela; Pelo, Elisabetta; Mannelli, Francesco; Guglielmelli, Paola; Vannucchi, Alessandro Maria
- Abstract
Motivation The past few years have seen the emergence of nanopore-based sequencing technologies which interrogate single molecule of DNA and generate reads sequentially. Results In this paper, we demonstrate that, thanks to the sequentiality of the nanopore process, the data generated in the first tens of minutes of a typical MinION/GridION run can be exploited to resolve the alterations of a human genome at a karyotype level with a resolution in the order of tens of Mb, while the data produced in the first 6–12 h allow to obtain a resolution comparable to currently available array-based technologies, and thanks to a novel probabilistic approach are capable to predict the allelic fraction of genomic alteration with high accuracy. To exploit the unique characteristics of nanopore sequencing data we developed a novel software tool, Nano-GLADIATOR, that is capable to perform copy number variants/alterations detection and allelic fraction prediction during the sequencing run ('On-line' mode) and after experiment completion ('Off-line' mode). We tested Nano-GLADIATOR on publicly available ('Off-line' mode) and on novel whole genome sequencing dataset generated with MinION device ('On-line' mode) showing that our tool is capable to perform real-time copy number alterations detection obtaining good results with respect to other state-of-the-art tools. Availability and implementation Nano-GLADIATOR is freely available at https://sourceforge.net/projects/nanogladiator/. Supplementary information Supplementary data are available at Bioinformatics online.
- Subjects
INTERNET servers; DNA copy number variations; SINGLE molecules; HUMAN genome; SOFTWARE development tools; NUCLEOTIDE sequencing
- Publication
Bioinformatics, 2019, Vol 35, Issue 21, p4213
- ISSN
1367-4803
- Publication type
Article
- DOI
10.1093/bioinformatics/btz241