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

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

Genetics
Molecular Medicine
Genetics(clinical)

Online availability

10.3389/fgene.2012.00320

Library availability

Discover UIUC Full Text

Cite this

@article{120d541032c54480af7eb870f1f3f26d,

title = "NSeq: A multithreaded Java application for finding positioned nucleosomes from sequencing data",

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.",

keywords = "Nucleosome, Nucleosome positioning",

author = "Abhinav Nellore and Konstantin Bobkov and Elizabeth Howe and Aleksandr Pankov and Aaron Diaz and Song, {Jun S.}",

year = "2013",

doi = "10.3389/fgene.2012.00320",

language = "English (US)",

volume = "3",

journal = "Frontiers in Genetics",

issn = "1664-8021",

publisher = "Frontiers Media S. A.",

number = "JAN",

}

TY - JOUR

T1 - NSeq

T2 - A multithreaded Java application for finding positioned nucleosomes from sequencing data

AU - Nellore, Abhinav

AU - Bobkov, Konstantin

AU - Howe, Elizabeth

AU - Pankov, Aleksandr

AU - Diaz, Aaron

AU - Song, Jun S.

PY - 2013

Y1 - 2013

N2 - 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.

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

UR - http://www.scopus.com/inward/record.url?scp=84876166912&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84876166912&partnerID=8YFLogxK

U2 - 10.3389/fgene.2012.00320

DO - 10.3389/fgene.2012.00320

M3 - Article

C2 - 23335939

AN - SCOPUS:84876166912

SN - 1664-8021

VL - 3

JO - Frontiers in Genetics

JF - Frontiers in Genetics

IS - JAN

M1 - Article 320

ER -

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

Abstract

Keywords

ASJC Scopus subject areas

Online availability

Library availability

Related links

Fingerprint

Cite this