Latest news
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;
- New standalone tools for read filtration based on k-mer coverage and estimating number of unique k-mers in reads;
- Improved SPAligner tool for read-to-graph alignment;
- Major performance improvements and memory consumption reduction in graph construction,simplification procedures and throughout the whole pipeline.
Full list can be found in changelog.
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”). Research fellows Alexey Gurevich and Alla Mikheenko took the first place in the category of “Contribution to science of young researchers” (for their work on genome assembly evaluation toolkit QUAST).
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”, 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). The course was created with the participation of Mikhail Rayko (Center for Algorithmic Biotechnology at St. Petersburg State University), Nikolai Vyahhi (Director of the Institute of Bioinformatics, St. Petersburg), Pavel Dobrynin and Ekaterina Chernyaeva (St. Petersburg State University).
According to experts, “like another St. Petersburg State University course on bioinformatics (“Introduction to Bioinformatics”), this course is excellent and very close to the gold standard. Educational information is presented in a simple, accessible form, but at the same time at a high scientific and methodological level.”
The course “Introduction to Bioinformatics: Metagenomics” is available on platforms Coursera, Stepik and “Open Education”. The course “Introduction to Bioinformatics” is available on the Coursera platform. More than 35 thousand students have already taken St. Petersburg State University bioinformatics courses.
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. More details are in the manual and our ISMB 2018 proceedings paper.
Download the tool here: https://sourceforge.net/projects/quast/files/ or simply install it via pip (pip install quast), Bioconda (conda install -c conda-forge -c bioconda quast) or Brewsci/bio (brew install quast). You can try the online version of our tool here.
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