UGENE NGS: The next step in a next generation sequencing bioinformatics toolkit

Friday, November 08, 2013 — Poster Session III
10:00 a.m. – 12:00 p.m.	FAES Academic Center (Upper-Level Terrace)	NIAID	GEN-12

Authors

R. Henderson
O. Golosova
A. Gabrielian
Y. Vaskin
V. Nagarajan
A. Oler
M. Quiñones
D. Hurt
G. German
M. Leerkes
D. Kandrov
Y. Huyen

Abstract

The NIAID Bioinformatics and Computational Biosciences Branch (BCBB) has partnered with Unipro to create a Next Generation Sequencing (NGS) version of UGENE, a free, open-source, cross-platform bioinformatics toolkit that runs on Windows, Mac OS, and Linux. This toolkit integrates pipelines for Variant Calling, RNA-Seq, and CHiP-Seq. The Variant Calling pipeline uses SAMtools to call SNPs and INDELs. The RNA-Seq pipeline uses the Tuxedo suite of NGS tools, including TopHat, Bowtie, and several tools from the Cufflinks package. The CHiP-Seq pipeline incorporates a workflow for Cistrome, a custom distribution of the Galaxy computational biology platform. Together, these pipelines form the NGS portion of UGENE NGS. The next step of UGENE NGS is cloud-based access to data with mobile apps. BCBB and Unipro are designing interfaces so that UGENE users will be able to retrieve genes, variants, and sequences from all publicly available BioMarts. In addition, support for the Distributed Annotation System (DAS) API is being tested, so that UGENE will include capabilities for annotating new unknown protein sequences from recently sequenced bacteria or viruses. Understanding these protein sequences will help researchers develop new defenses for preventing the transmission of infectious diseases.