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SPAdes 2.4 is released

Submitted by andrey on 28 Feb 2013, Thu, 13:50

Another version of SPAdes single-cell assembler has been just released. 

The main feature in this version is mismatch correction module, which allows to reduce mismatch and short indel rates in resulting contigs and scaffolds.
 
SPAdes 2.4 now also includes rectangle graph algorithm as an optional repeat resolution module (which can be used instead of the standard one). Rectangle graph algorithm was previously released separately from SPAdes, which made the tool harder to use. Now you can try it just by setting a single option in SPAdes.
 
Additionally, we decreased memory consumption in read error correction module, improved assembly quality of standard isolate data sets and fixed some small bugs, some of which were reported by our users. Thank you for your feedback!
 
And finally, some good news for Mac users — we now have SPAdes binaries for Mac OS.
 
You can download SPAdes 2.4 here.

New frontiers for genome assembly quality assessment

Submitted by Nikolay Vyahhi on 18 Feb 2013, Mon, 18:15

http://de.wikipedia.org/wiki/Pinsel#SpezialpinselThree good news on QUAST web-service and command line tool, which evaluates a quality of genome assemblies by computing various metrics and providing nice reports:

1. "QUAST: Quality Assessment Tool for Genome Assemblies" paper was accepted to Bioinformatics, now you can cite it in your papers using this BibTeX.

2. We've released QUAST 2.1 with new options, new speed-ups and improved indels counting.

3. QUAST was downloaded more than 1000 times with most of downloads from Russia and US.

Sibelia Interactive Examples

Back to Sibelia webpage.


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QUAST 2 for assembly quality assessment

Submitted by Nikolay Vyahhi on 19 Jan 2013, Sat, 17:33

The new major version of QUAST (QUality ASsesment Tool for Genome Assembly) was released by the lab. Adjustable, scalable, and more accurate, see changelog for details.

You can download it on Sourceforge, or try out online at the QUAST web-server.

Sibelia 2.1: optimized version for many genomes!

Submitted by Nikolay Vyahhi on 17 Jan 2013, Thu, 20:34

Sibelia 2.1 incorporates optimizations for case of many genomes and the trimming procedure that improves blocks boundaries precision.

SPAdes Download

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Thank you!

Rectangle Graph Module released

Submitted by Nikolay Vyahhi on 11 Jan 2013, Fri, 09:43

Stable version of the Rectangle Graph Module for Repeat Resolution in Genome Assembly was released!

Though the specific implementation of the idea of the rectangle graph approach is already included into the current SPAdes distribution, we're also releasing the Rectangle Graph Module (RGM) as the separate code which can be run independently of SPAdes.

RGM can be run with other genome assemblers if they use the graph format as SPAdes files.

SiBELia 2.0 is out

Submitted by Nikolay Vyahhi on 29 Nov 2012, Thu, 00:48

Comparative genomic tool Sibelia 2.0 is here! With improved performance and new interactive circular visualization for web.

 

Joint meeting with Theodosius Dobzhansky Center for Genome BioInformatics

Submitted by Nikolay Vyahhi on 11 Nov 2012, Sun, 17:00

Lab members have met with members of Theodosius Dobzhansky Center for Genome BioInformatics at the St. Petersburg State University.

Details of the meeting.

SPAdes 2.3 released, now with scaffolding

Submitted by Nikolay Vyahhi on 1 Nov 2012, Thu, 10:48

You can download SPAdes 2.3 from http://bioinf.spbau.ru/spades, see new manual and the changelog.

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