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A paper on ExSPAnder—a universal repeat resolution algorithm in SPAdes—is out

The recent version of SPAdes assembler was introduced with a novel universal repeat resolution method – ExSPAnder. The algortihm works accurately in the case of both single and multiple libraries of read-pairs in both standard and single-cell assembly projects.


SPAdes 3.1 is out!

We just released SPAdes 3.1 with several improvements and bugfixes:
- Mate-pairs only assembly (for high-quality mate-pair libraries like Illumina NexteraMP)
- Unmapped BAM file support (like the ones produced from Torrent Server)
- Improved IonTorrent pipeline
- Fixed dipSPAdes bugs and user interface
- Better assemblies with mate-pair libraries
- Improved performance of repeat resolution module
Download new version at

SPAdes on BaseSpace: one-click assembly on cloud

Illumina announced SPAdes realease in their cloud-computing environment BaseSpace.

BaseSpace is the first cloud environment directly integrated into Illumina industry-leading sequencing platform. It allows sequencing labs easily and securely analyze, archive, and share sequencing data.

Now SPAdes assembler is integrated into the platform and can be used as a one-button solution for de novo assembly of small genomes. The output includes assembly quality statistics provided by QUAST.

QUAST 2.3 released

Long-awaited contig alignment plots (see an example below), updated misassemblies detection logic, full report in PDF format, and many other features included!

See Changes for for a full list of new features and fixed bugs.

See new version of Manual including new options and reports descriptions and FAQ section.

All other news and useful links are presented on QUAST page.
You can download QUAST 2.3 and previous versions here.

SPAdes 3.0 is out

Now with support for IonTorrent, PacBio, module for highly polymorphic diploid genomes and many other new features. Check out the details here.

Galaxy wrapper for SPAdes 2.5.1 is released

Thanks to our user Lionel Guy, now it is possible to integrate SPAdes into Galaxy pipelines seamlessly. Wrapper is available on Galaxy Tool Shed at

SPAdes 2.5.1 is released

We are happy to announce that the version 2.5.1 of SPAdes single-cell assembler has been released. 

This version contains mostly minor improvements and fixes:

  • more user-friendly error reports,
  • less misassemblies on single-cell data sets with low covered genome fraction,
  • decreased memory consumption during the error correction stage.

The release also contains new features:

  • running SPAdes from check points: one can restart the assembler after a crash without running finished steps once again,
  • automatic k-mer size selection for standard data sets using the maximal read length.

You can download SPAdes 2.5.1 here.

Pavel Pevzner finished the first lection on Bioinformatics Algorithms for Coursera

Is St. Petersburg, Pavel Pevzner finished his first lection for the Coursera's Bioinformatics Algorithms.

The course will cover common algorithms underlying the fundamental topics in bioinformatics: genome assembly, comparing DNA and protein sequences, finding genes and regulatory motifs, analyzing gene expression, constructing evolutionary trees, analyzing genome rearrangements, and identifying proteins.

The instructors are the Lab's leading scientist Pavel Pevzner, Phillip E. C. Compeau, and the creator of Rosalind Nikolay Vyahhi.


via @bioinforussia.

Final summer internship presentation

The final presentation of the summer internship projects took place on 6 September in the Academic University.


Artem Tarasov: Utilizing referenece genomes for assembly refinement.



Petar Ivanov: Applying chimeric read information for genome assembly.



Vitaliy Demyanuk: Antibody sequencing from mass spectra.


Summer School for Bioinformatics

The Summer School of the Bioinformatics Institute took place in Moscow at the beginning of August.

The school was dedicated to genome and transcriptome analysis, NGS, epigenetics, comparative genomics and molecular evolution. In addition to general lections on bioinformatics, there were special courses aimed to improve programming skills for biologists, and on the other hand, teach computer scientists molecular biology and biotechnologies.

биологи и информатики

Lab's members Alla Lapidus, Andrey Prjibelsky and Pavel Pevzner took part in preparing the school curriculum. Moreover, lectures were given by Sergey Nurk, Alexey Gurevich, Anton Korobeynikov, Alla Lapidus and Andrey Prjibelsky.




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