Work

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

Year: 2013

Type: article

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.

Source: Frontiers in Genetics

DOI: 10.3389/fgene.2012.00320

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

Institution: University of California, San Francisco

Language: English

Topic: Genomics and Chromatin Dynamics

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $3,801