ngs.plot

https://github.com/shenlab-sinai/ngsplot

Methods

linear multiple view single scale multiple focus contiguous no abstraction no arrangement within interconnection segment contiguous type

Tool

Access Format programming language
Supported Files txttab sambamcram other
License GNU GENERAL PUBLIC LICENSE
Tool name

ngs.plot
Tool Link https://github.com/shenlab-sinai/ngsplot
Documentation https://github.com/shenlab-sinai/ngsplot

Paper

ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases

Shen, L., Shao, N., Liu, X. and Nestler, E., 2014. ngs. plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases. BMC genomics, 15(1), p.284.

Abstract

Background: Understanding the relationship between the millions of functional DNA elements and their protein regulators, and how they work in conjunction to manifest diverse phenotypes, is key to advancing our understanding of the mammalian genome. Next-generation sequencing technology is now used widely to probe these protein-DNA interactions and to profile gene expression at a genome-wide scale. As the cost of DNA sequencing continues to fall, the interpretation of the ever increasing amount of data generated represents a considerable challenge. Results: We have developed ngs.plot – a standalone program to visualize enrichment patterns of DNA-interacting proteins at functionally important regions based on next-generation sequencing data. We demonstrate that ngs.plot is not only efficient but also scalable. We use a few examples to demonstrate that ngs.plot is easy to use and yet very powerful to generate figures that are publication ready. Conclusions: We conclude that ngs.plot is a useful tool to help fill the gap between massive datasets and genomic information in this era of big sequencing data.