Latest news
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
Онлайн-курс «Введение в биоинформатику: метагеномика», автором и руководителем которого является профессор СПбГУ, заместитель директора Центра алгоритмической биотехнологии Алла Львовна Лапидус, стал победителем IV международного конкурса EdCrunch Award 2018 в номинации «За способность понятно объяснять самые абстрактные идеи» (http://edtek.pro/award/pobediteli-2018.php). В разработке курса приняли участие Михаил Райко (сотрудник Центра алгоритмической биотехнологии СПбГУ), Николай Вяххи (директор Института биоинформатики (СПб), Павел Добрынин и Екатерина Черняева (сотрудники СПбГУ).
По мнению экспертов “как и другой курс СПбГУ по биоинформатике (“Введение в биоинформатику”), данный курс превосходен и близок к эталону. Учебная информация подается в простой, доступной форме, но при этом на высоком научно-методическом уровне”.
Курс «Введение в биоинформатику: метагеномика» размещен на платформах Coursera, Stepik и «Открытое образование». Курс «Введение в биоинформатику” доступен на международной платформе Coursera. Более 35 тысяч слушателей прошли обучение на курсах биоинформатики СПбГУ.
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.
SPAdes 3.12 is released
We are proud to announce a new version of SPAdes. SPAdes 3.12 contains several major improvements:
- Support for merged paired-end reads
- Experimental version of hybrid metagenome assembly pipeline
- The stand-alone useful tools: k-mer counting, assembly graph construction and alingner for long reads to the graph
- Performance improvements
Full list can be found in changelog
Web of Science Awards 2017
A research fellow from the Center for Algorithmic Biotechnology, Alexey Gurevich, has been honored with the Web of Science Award 2017 for his work on SPAdes, QUAST and Dereplicator projects. This annual award is presented to honor Russian individual researchers and organisations in various fields of study that have the largest number of highly cited publications in Web of Science Core Collection in the preceding year. See more details in St. Petersburg State University press release (in Russian).
This is the second award of this kind granted to the members of the Center. Back in 2015 Dr. Alla Lapidus (Deputy director of the Center for Algorithmic Biotechnology) was honored with the Elsevier Scopus Award 2015 for her outstanding achievement in the field of Biology. This award recognizes the contributions made by Russian researchers to the global scientific landscape and is based on the publication and citation data drawn from Elsevier’s Scopus.
rnaQUAST 1.5 is released!
A new version of rnaQUAST contains important fixes of several usability problems detected by our users.
rnaQUAST is a software for quality evaluation of de novo transcriptome assemblies using reference genome and gene database.
SPAdes 3.11 is released!
A new version of SPAdes is finally out. In this release you will see many nice improvements, e.g.
- Reworked IonHammer module
- Major improvements in metaSPAdes pipeline
- Support for strand-specific data and coverage-based isoform detection in rnaSPAdes
- exSPAnder repeat resolution is improved in terms of both performance and repeat resolution accuracy
- Better RAM consumption and running time in general
- Improved careful mode for isolate datasets
- Several important bug-fixes
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