metaFlye is a new metagenomic-specific version of the Flye long-read genome assembler (ONT and PacBio sequencing).
The paper about the assembler and its application to real and simulated metagenomic datasets is out in Nature Methods (see SPbU press releases in Russian and English). The research project is a result of a collaboration of 11 Russian and American scientists which included two members of our laboratory,
T2T Consortium presented first complete human genome assembly on T2T/HPRC Open Science Days! Polished version of the assembly can be found on github. This is exciting breakthrough for all bioinformatics community!
We are proud that members of our laboratory take part in this important initiative, especially, Alla Mikheenko and Alexey Gurevich,
The fourth international conference “Bioinformatics: from Algorithms to Applications” (BiATA2020) moved online this year and was accompanied by a 2-day workshop on metagenomic data analysis. All pre-recorded talks are available online and can be found on BiATA2020 website.
We thank all speakers for presenting their great work and looking forward to the next year!
We are delighted to present novel SPAdes assembler mode — coronaSPAdes, created by our researchers Anton Korobeynikov and Dmitry Meleshko. CoronaSPAdes allows to assemble full-length coronaviridae genomes from the transcriptomic and metatranscriptomic data. For more details visit coronaSPAdes official page.
We hope that coronaSPAdes will accelerate the ongoing coronavirus research!
EMBL-EBI presented the latest version of the MGnify 5 pipeline, which now uses metaSPAdes for all metagenome assemblies. Check out new version at EMBL-EBI website here. More detailed information on the latest release can be found in the original paper.
Congratulations to Anton Korobeynikov and all members of our laboratory,
First complete genome sequence of coronavirus SARS-CoV-2 from a Russian patient was sequenced by the scientific group from Smorodintsev Research Institute of Influenza in collaboration with members of our laboratory Michael Rayko and Dmitry Antipov. The sequence, named hCoV-19/Russia/StPetersburg-3524/2020, is available via GISAID.
See more details in N+1 (in Russian)
Members of the Center for Algorithmic Biotechnology were honored with St. Petersburg University annual scientific and educational awards (see all winners in Russian). Research Fellow Michael Rayko took the first place in the category of “Educational and methodical work” (for the SPbU Coursera online course “Introduction to Bioinformatics: Metagenomics”).
Members of the Center for Algorithmic Biotechnology were honored with St. Petersburg University annual scientific and educational awards (see all winners in Russian). Junior Research Fellow Dmitry Meleshko and Leading Research Fellow Anton Korobeynikov took the first place in the category of “Contribution to science of young researchers” (for their paper “MetaSPAdes: a new versatile metagenomic assembler“).
Finally, SPAdes 3.14 is out! This release includes such new features as:
- BiosyntheticSPAdes pipeline for identifying Biosynthetic Gene Clusters (BGCs);
- Hybrid transcriptome assembly (Illumina RNA-Seq + Iso-seq / ONT RNA);
- Plasmid assembly from metagenomic datasets;
- New –isolate option that improves assembly quality of standard datasets with high coverage;
Members of the Center for Algorithmic Biotechnology were honored with St. Petersburg University annual scientific and educational awards (see all winners in Russian). Deputy director of the Center Dr. Prof. Alla Lapidus took the first place in the category of “Educational and methodical work” (for the first SPbU Coursera online course “Introduction to Bioinformatics”).