Visualization of Nanopore Sequencing Data in Metagenomics

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Nanopore sequencing holds great promise in the field of metagenomics – the study of genomes of microbial organisms sharing the same environment. Its low cost, the length of reads and the size of the sequencing device MinION, which can easily fit into a palm, make nanopore sequencing the ideal fit for metagenomics. However, one of the major questions in metagenomics still stays unresolved – after a shotgun sequencing run, how are we able to determine which sequences belong to the same taxonomical unit? The current techniques trying to solve this issue are based on extraction of selected features from each of the sequences followed by a suitable clustering algorithm, which in an ideal case produces clusters containing sequences that belong to the same operational taxonomic unit (OTU). This process is commonly called binning. Based on the number of extracted features, the visualization of the sequences in the form of points in 2D or 3D space can be included in the final pipeline to make the results human-comprehensible. Here we present a novel method for visualization of metagenomic sequences, which works with the original electric current signals, so-called “squiggles”, produced by nanopore sequencing, instead of working with the final character string sequence obtained after base-calling. Apart from the fact that we do not need the prior base-calling, the algorithm runs with linear time complexity, which allows almost instant results. We tested the algorithm on a simplified metagenome available in the EBI Metagenomics database and obtained reliable results

nanopore sequencing, Hjorth descriptors, binning, metagenomics, signal processing

KUPKOVÁ, K.; PROVAZNÍK, I.; SEDLÁŘ, K.; HON, J.; MARTÍNEK, T.; ZENDULKA, J.

21. 7. 2017

Praha

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https://www.iscb.org/cms_addon/conferences/ismbeccb2017/posterlist.php?cat=D