Foundation of Croatian Academy of Sciences and Arts awards financial support to CIR's research assistant Ivan Sović
By the decision of the Executive board of the Foundation of Croatian Academy of Sciences and Arts from 08.09.2015. financial support of 5000HRK has been approved for the project "Methods for alignment and assembly of DNA sequences using nanopore sequencing data". The project was proposed by Ivan Sović, a research assistant in the Centre for Informatics and Computing, RBI. The topic of the project is tightly related to the scope of his Ph.D. thesis.
The main goal of the project is to develop fast, efficient and accurate algorithms for alignment and de novo assembly of genomic sequencing reads, with a strong focus on the third generation sequencing data. The third generation is especially interesting because of the newest technology made available by Oxford Nanopore, whose devices are very small in size (connect through USB 3.0 interface; the size of a cell phone; the devices produced by competing companies can weigh up to 1000kg), the price of several orders of magnitude lower than the competition, and they enable acquisition of large amounts of data, but unfortunately with a large error rate. The existing algorithmic methods are not sensitive enough to successfully handle very long reads (~10000bp and longer) with such high error rates (~30%). As a preliminary result of the project, a very accurate and sensitive method for mapping/alignment of nanopore sequencing reads has been developed under the name "GraphMap": http://biorxiv.org/content/early/2015/06/10/020719. The method is implemented and publically available under the MIT licence, and can be accessed on the following address: https://github.com/isovic/graphmap.git.