Algorithmic Biology Lab

New SPAdes 3.5 is out!

This release includes new mismatch correction module, support for Oxford Nanopore and Lucigen NxMate mate-pair libraries, possibility to specify coverage cutoff, improved performance and several fixes.

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

http://bioinf.spbau.ru/en/spades

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".

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.

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 http://bioinf.spbau.ru/en/spades

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

http://blog.basespace.illumina.com/2014/05/07/push-button-de-novo-assembly-with-the-spades-assembler-3-0

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.

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.

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 http://toolshed.g2.bx.psu.edu/view/lionelguy/spades

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.