AUTHOR=Nellore Abhinav , Bobkov Konstantin , Howe Elizabeth , Pankov Aleksandr , Diaz Aaron , Song Jun S.

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

JOURNAL=Frontiers in Genetics

VOLUME=3

YEAR=2013

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2012.00320

DOI=10.3389/fgene.2012.00320

ISSN=1664-8021

ABSTRACT=<p>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 <ext-link ext-link-type="uri" xlink:href="https://github.com/songlab/NSeq" xmlns:xlink="http://www.w3.org/1999/xlink">https://github.com/songlab/NSeq</ext-link>. The software is supported on all major platforms equipped with Java Runtime Environment 6 or later.</p>