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

Abhinav Nellore; Konstantin Bobkov; Elizabeth Howe; Aleksandr Pankov; Aaron Diaz; Jun S. Song

doi:10.3389/fgene.2012.00320

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

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

Research output: Contribution to journal › Article › peer-review

10 Scopus citations

Abstract

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.

Original language	English (US)
Article number	Article 320
Journal	Frontiers in Genetics
Volume	3
Issue number	JAN
DOIs	https://doi.org/10.3389/fgene.2012.00320
State	Published - 2013
Externally published	Yes

Keywords

Nucleosome
Nucleosome positioning

ASJC Scopus subject areas

Molecular Medicine
Genetics
Genetics(clinical)

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10.3389/fgene.2012.00320

Cite this

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abstract = "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.",

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AU - Pankov, Aleksandr

AU - Diaz, Aaron

AU - Song, Jun S.

PY - 2013

Y1 - 2013

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AB - 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.

KW - Nucleosome

KW - Nucleosome positioning

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

Abstract

Keywords

ASJC Scopus subject areas

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