metaSPAdes in the latest MGnify pipeline!

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,

SPbU Awards 2019 in Education

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”).

SPAdes 3.14 is out now!

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;

SPbU Awards 2018

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”).

SPAdes 3.13 is released

New SPAdes 3.13 includes significant improvements in rnaSPAdes pipeline and several important fixes.

Note, that dipSPAdes is not supported anymore and was removed from SPAdes package.

Full list can be found in changelog.

EdCrunch Award 2018

Online course “Introduction to Bioinformatics: Metagenomics” is one of the best in Russia and the CIS.
Online course “Introduction to Bioinformatics: Metagenomics”, authored and led by Professor of St. Petersburg State University, Deputy Director of the Center for Algorithmic Biotechnology Alla L. Lapidus, is a winner of the 4th international competition EdCrunch Award 2018 in the nomination “For the ability to clearly explain the most abstract ideas” (http://edtek.pro/award/pobediteli-2018.php — in Russian). 

QUAST 5.0 is released!

We are happy to announce a long-awaited major release of QUAST! QUAST 5.0.0 includes QUAST-LG (mode for evaluating large genome assemblies) and many other new features:

  • New k-mer-based completeness and correctness metrics
  • Enhanced reference-free analysis using BUSCO assessments
  • The concept of upper bound assembly (theoretical limits on the assembly completeness and contiguity for a given genome and set of reads)

The full list of changes is here.