Journal Article

MicroRazerS: rapid alignment of small RNA reads

Anne-Katrin Emde, Marcel Grunert, David Weese, Knut Reinert and Silke R. Sperling

in Bioinformatics

Volume 26, issue 1, pages 123-124
Published in print January 2010 | ISSN: 1367-4803
Published online October 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp601
MicroRazerS: rapid alignment of small RNA reads

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Motivation: Deep sequencing has become the method of choice for determining the small RNA content of a cell. Mapping the sequenced reads onto their reference genome serves as the basis for all further analyses, namely for identification and quantification. A method frequently used is Mega BLAST followed by several filtering steps, even though it is slow and inefficient for this task. Also, none of the currently available short read aligners has established itself for the particular task of small RNA mapping.

Results: We present MicroRazerS, a tool optimized for mapping small RNAs onto a reference genome. It is an order of magnitude faster than Mega BLAST and comparable in speed with other short read mapping tools. In addition, it is more sensitive and easy to handle and adjust.

Availability: MicroRazerS is part of the SeqAn C++ library and can be downloaded from http://www.seqan.de/projects/MicroRazerS.html.

Contact: emde@inf.fu-berlin.de; grunert@molgen.mpg.de

Journal Article.  1609 words. 

Subjects: Bioinformatics and Computational Biology

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