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 journalArticle

7 Citations (Scopus)

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 languageEnglish (US)
Article numberArticle 320
JournalFrontiers in Genetics
Volume3
Issue numberJAN
DOIs
StatePublished - 2013
Externally publishedYes

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Nucleosomes
Software
DNA

Keywords

  • Nucleosome
  • Nucleosome positioning

ASJC Scopus subject areas

  • Molecular Medicine
  • Genetics
  • Genetics(clinical)

Cite this

NSeq : A multithreaded Java application for finding positioned nucleosomes from sequencing data. / Nellore, Abhinav; Bobkov, Konstantin; Howe, Elizabeth; Pankov, Aleksandr; Diaz, Aaron; Song, Jun S.

In: Frontiers in Genetics, Vol. 3, No. JAN, Article 320, 2013.

Research output: Contribution to journalArticle

Nellore, Abhinav ; Bobkov, Konstantin ; Howe, Elizabeth ; Pankov, Aleksandr ; Diaz, Aaron ; Song, Jun S. / NSeq : A multithreaded Java application for finding positioned nucleosomes from sequencing data. In: Frontiers in Genetics. 2013 ; Vol. 3, No. JAN.
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