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SPAdes 3.1.1: a bug fix release

Introduced several improvements in IonHammer; fixed minor bugs in repeat resolution and scaffolding.


ExSPAnder won the Outstanding Paper Award at ISMB!

The paper "ExSPAnder: a universal repeat resolver for DNA fragment assembly" won the Outstanding Student Paper award at ISMB 2014! Congratulations to Andrey D. Prjibelski and Irina Vasilinetc.

The award is given to the undergraduate, Master’s or PhD student who presents the most thought-provoking or original paper at the Conference, as judged by the panel of experts.

ISMB 2014, the conference on computational biology took place in Boston at July 11–15, 2014. In addition to the paper, the Lab also presented a poster on SPAdes 3.0: "New Features in SPAdes Genome Assembler".

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.

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