JCVI used SPAdes in their study of Porphyromonas gingivalis

Submitted by kira on 8 Apr 2013, Mon, 19:58

A team of researchers led by scientists from the J. Craig Venter Institute (JCVI) successfully applied SPAdes in their breakthrough study outlining the recovery and genomic analysis, using single-cell genomic techniques, of a periodontal pathogen, Porphyromonas gingivalis, from a hospital sink. The team, led by JCVI’s Jeffrey McLean published their study in the April 5, 2013 edition of the journal Genome Research.

http://genome.cshlp.org/content/early/2013/03/27/gr.150433.112.abstract

JCVI press release

 

The Sanger Institute used SPAdes in their study of Chlamydia trachomatis

Submitted by kira on 8 Apr 2013, Mon, 19:54

The Sanger Institute used SPAdes in the first large single cell study of clinical pathogens for Chlamydia trachomatis beingresponsible for sexually transmitted infections and the blinding disease trachoma, which affect hundreds of millions of people worldwide.The results obtained by the group of researchers led by Nicholas R. Thomson appeared in Genome Research on March 22, 2013.

http://genome.cshlp.org/content/early/2013/03/21/gr.150037.112

Rosalind will be used for a Coursera course

Submitted by kira on 8 Apr 2013, Mon, 19:35

Rosalind will be used for an online Bioinformatics Algorithms course on Coursera to be given by Dr. Pavel Pevzner in Fall 2013.

Rosalind is named the Best Bioinformatics Educational Resource of 2012

Submitted by kira on 8 Apr 2013, Mon, 19:32

The bioinformatics blog www.homolog.us named Rosalind the Best Educational Resource in the article "Top Bioinformatics Contributions of 2012".

Rosalind receives a $25,000 grant

Submitted by kira on 8 Apr 2013, Mon, 19:27

The Rosalind educational portal recieves a $25,000 grant from Yuri Milner and Pavel Durov in the frame of "Start Fellows" project. 

http://www.ferra.ru/ru/techlife/news/2013/03/14/Start-Fellows-new-research-grants/

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.

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.

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.

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