metaFlye the Collector for reading genomes of microbic communities

Main articles:

• Genome
• DNA sequencing

2020: metaFlye presentation

On October 7, 2020 the SPbSU reported that the staff of Center of Algorithmic Biotechnology laboratory developed SPbSU as a part of group of the Russian and American scientists the collector of metaFlye specializing in assembly of DNA samples of microbic communities. With its help it is possible to solve a wide range of fundamental and applied tasks among which — control of process of treatment of the person and even creation of new drugs.

For studying of DNA of any live organism scientists of the whole world use difficult biotechnology tools — sequenators. These special machines are not able "read" a genome from beginning to end (as people read books). They do it by separate short fragments — readings, or rida (from the English word read). Consolidation of readings in longer fragments, and ideally — in the uniform sequence of an initial genome, represents extremely difficult computing task, something the reminding assembly of a puzzle from millions of fragments. The task is complicated by the fact that genomes often contain a large number of identical recurrent sequences which quite often exceed length of readings. Specialized programs — genomic collectors help to cope with this difficult task.

Several dozens of different collectors who develop in the leading bioinformatichesky laboratories worldwide are available to scientists. Such variety is caused by the fact that the algorithms which are the cornerstone of collectors need to be adapted to different types of the input data obtained on different types of sequenators and also to different organisms. For example, approaches can not be suitable for assembly of a genome of bacteria to assembly of human genome at all and vice versa. Besides, developers of genomic collectors constantly aim to improve the solutions that their programs worked quicker, used less memory, and final assemblies were more long and more precisely, than at competitors.

The collector of metaFlye is used at assembly of metagenomes, i.e. DNA samples of the microbic communities received from different environments — for example, from depths of the ocean, soil in the park or intestines of the person. Receiving assembly of such sample, it is possible to define that for organisms in it they are provided and how many. Using the additional analysis of assembly, it is often possible to find out, than these organisms can eat as interact what substances synthesize. All these data can be used further, for example, for search of new medicines of natural origin, for determination of the reasons which are the cornerstone of special fertility of the soil when checking the course of treatment of the person and in a set of other both fundamental, and applied tasks.

The collector of metaFlye is intended for the data obtained on the most modern technology of sequencing at the moment — technologies of sequencing by long readings (long-read sequencing). For data of metagenomic sequencing (short-read sequencing, or next-generation sequencing, NGS) on the Illumina platform already several collectors used around the world are short readings. Their number includes the collector of metaSPAdes developed in the Center of algorithmic biotechnology of SPbSU in 2016. Also there are already programs for assembly of separate genomes from long readings. The product metaFlye allows to use features of technology for difficult metagenomic data. This is the first specialized collector for metagenomes working with Oxford Nanopore and PacBio technologies.

As incentive to creation of metaFlye the absence of the specialized metagenomic collector for technology of long readings served. This technology already cardinally changed all modern genomic science, we learned to receive much more complete assemblies. So, for example, with its help many missing fragments of human genome were read and localized recently (using the original Flye tool and too with participation of members of our laboratory). But for metagenomes such data only began to appear, and, of course, they demanded special tools, — one of authors of the project, the senior research associate of the Center of algorithmic biotechnology of SPbSU Mikhail Rayko notes

Work on metaFlye began about two years ago. If to reckon from creation of his predecessor, the genomic collector of Flye based on which the new project was implemented it turns out twice more — four years.

In our research published in the Nature Methods magazine we used metaFlye and other collectors to analyze a little simulated (i.e. generated on the computer, without sequencing of this DNA) and real metagenomic samples from digestive tract of the person, a cow and a sheep. Perhaps, the microbiome sample of a sheep as it was for the first time received and studied in this work while initial data of sequencing for two other samples are taken from works of third-party authors is of the greatest interest. Thanks to metaFlye in this sample it was succeeded to collect 10 times more virus genomes one and a half times more plasmids, than when using the best of the existing programs analogs, — the senior research associate of the Center of algorithmic biotechnology of SPbSU Alexey Gurevich tells

Other curious result was the fact that in a sample it was succeeded to collect genomes not only bacteria and the Archean, but also eukariot. At the same time the bioinformatichesky analysis showed that nearly a half of eukaryotic genomic fragments concerns representatives of nematodes, or roundworms. This result completely corresponds to the report on opening of a corpse of an animal in which symptoms of a parasitic infection were detected.

The publication about metaFlye — result of collaboration of 11 Russian and American scientists representing St. Petersburg State University, the University of California to San Diego (UCSD), Institute of bioinformation science (St. Petersburg) and the American research centers of dairy and meat products. The collector of metaFlye is generally developed in UCSD. His creator and the original author of the publication — Mikhail Kolmogorov, post-dock of UCSD. The research supervisor of the project — Pavel Pevzner, professor of UCSD and the chief scientific consultant of the Center of algorithmic biotechnology of SPbSU.