CGB: A UNIX shell program to create custom instances of the UCSC Genome Browser

TL;DR

This paper introduces CGB, a UNIX shell program that automates the creation of custom UCSC Genome Browser instances for non-UCSC genomes, simplifying setup and enhancing security.

Contribution

It presents a novel automation tool that streamlines creating secure, customized genome browser instances for researcher-generated sequences.

Findings

Automates genome browser setup process

Provides password protection for custom instances

Successfully applied to bacterial genome data

Abstract

The UCSC Genome Browser is a popular tool for the exploration and analysis of reference genomes. Mirrors of the UCSC Genome Browser and its contents exist at multiple geographic locations, and this mirror procedure has been modified to support genome sequences not maintained by UCSC and generated by individual researchers. While straightforward, this procedure is lengthy and tedious and would benefit from automation, especially when processing many genome sequences. We present a Unix shell program that facilitates the creation of custom instances of the UCSC Genome Browser for genome sequences not being maintained by UCSC. It automates many steps of the browser creation process, provides password protection for each browser instance, and automates the creation of basic annotation tracks. As an example we generate a custom UCSC Genome Browser for a bacterial genome obtained from a massively parallel sequencing platform.