Methods ARTICLE

Front. Genet., 11 January 2013 | doi: 10.3389/fgene.2012.00320

NSeq: a multithreaded Java application for finding positioned nucleosomes from sequencing data

Abhinav Nellore1,2, Konstantin Bobkov1,2, Elizabeth Howe1,2, Aleksandr Pankov1,2, Aaron Diaz1,2 and Jun S. Song1,2,3,4*
  • 1Institute for Human Genetics, University of California, San Francisco, CA, USA
  • 2The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, USA
  • 3Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
  • 4Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA

We introduce NSeq, a fast and efficient Java application for finding positioned nucleosomes from the high-throughput sequencing of MNase-digested mononucleosomal DNA. NSeq includes a user-friendly graphical interface, computes false discovery rates (FDRs) for candidate nucleosomes from Monte Carlo simulations, plots nucleosome coverage and centers, and exploits the availability of multiple processor cores by parallelizing its computations. Java binaries and source code are freely available at https://github.com/songlab/NSeq. The software is supported on all major platforms equipped with Java Runtime Environment 6 or later.

Keywords: nucleosome, nucleosome positioning

Citation: Nellore A, Bobkov K, Howe E, Pankov A, Diaz A and Song JS (2013) NSeq: a multithreaded Java application for finding positioned nucleosomes from sequencing data. Front. Gene. 3:320. doi: 10.3389/fgene.2012.00320

Received: 13 November 2012; Paper pending published: 29 November 2012;
Accepted: 21 December 2012; Published online: 11 January 2013.

Edited by:

Xiangqin Cui, University of Alabama at Birmingham, USA

Reviewed by:

Joo Chuan Tong, Institute for Infocomm Research, Singapore
Cenny Taslim, The Ohio State University, USA

Copyright © 2013 Nellore, Bobkov, Howe, Pankov, Diaz and Song. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in other forums, provided the original authors and source are credited and subject to any copyright notices concerning any third-party graphics etc.

*Correspondence: Jun S. Song, Institute for Human Genetics, University of California, San Francisco, CA, USA. e-mail: songj@humgen.ucsf.edu

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