Galaxy

From UABgrid Documentation
Revision as of 15:30, 7 March 2013 by Curtish@uab.edu (Talk | contribs)

Jump to: navigation, search

Contents


Overview

The UAB Galaxy platform for experimental biology and comparative genomics designed to help you analyze multiple alignments, compare genomic annotations, profile metagenomic samples and more from your web browser. This platform is built on Galaxy, backed by the Cheaha compute cluster, and powered by UABgrid.

The primary uses of UAB Galaxy are to provide a simple web interface for NGS (short read sequencing) analysis for genomic and transcriptomic datasets, using tools like BWA, Bowtie, Tophat and Cufflinks, as well as simple sequence manipulation via the EMBOSS toolkit.

Using Galaxy / Tutorials

There are numerous general tutorials online at the Penn State public Galaxy site that are worth looking at.

There are also several UAB tutorials on NGS Analysis with Galaxy, created for HPC Boot Camp 2011 and a nice talk by Jeremy Goecks during Research Computing Day 2011.

Galaxy@UAB

The UAB Galaxy instance can be accessed at https://galaxy.uabgrid.uab.edu using BlazerID credentials. No account on the cluster is needed. However, the tools installed for galaxy (BWA, etc) can be accessed via the command line if you have an account on the cluster.

Available Tools

Following is a short list highlighting some of the important tools available:

Software Version Information
bwa 0.5.9-r26 Align genomic short reads to a reference genome
bowtie 0.12.7 Align genomic short reads to a reference genome
samtools 0.1.12a Alignment (SAM/BAM file) manipulations
velvet 1.1.03 Denovo Assembly
Top Hat 1.4.0 Align transcriptome short reads to a reference genome
Cuff Links 1.3.0 Reconstruct and quantify transcript levels from tophat alignments.
EMBOSS 6.3.1 European Molecular Biology Open Software Suite - sequence manipulation and format conversion


Installed Genome Indexes

You can always use your own genome by uploading the .fasta into your history, but alignments against installed (pre-indexed) genomes run much more quickly. If you need an additional genome installed, please contact [1].

dbkey Genome Accessions
mm9 Mouse July 2007 (NCBI37/mm9) (mm9)
mm10 Mouse Dec. 2011 (GRCm38/mm10) (mm10)
hg18 Human Mar. 2006 (NCBI36/hg18) (hg18)
hg19 Human Feb. 2009 (GRCh37/hg19) (hg19)
sacCer2 S. cerevisiae June 2008 (SGD/sacCer2) (sacCer2)
sacCer3 S. cerevisiae Apr. 2011 (SacCer_Apr2011/sacCer3) (sacCer3)
ce10 C. elegans Oct. 2010 (WS220/ce10) (ce10)
rn4 Rat Nov. 2004 (Baylor 3.4/rn4) (rn4)
rn5 Rat Mar. 2012 (RGSC 5.0/rn5) (rn5)
danRer7 Zebrafish Jul. 2010 (Zv9/danRer7) (danRer7)
eschColi_APEC_O1 Escherichia coli APEC O1 chr=5082025
eschColi_CFT073 Escherichia coli CFT073 chr=5231428
eschColi_EC4115 Escherichia coli EC4115 chr=5572075,plasmid_pO157=94644,plasmid_pEC4115=37452
eschColi_K12 Escherichia coli K12 chr=4639675
eschColi_EDL993 Escherichia coli O157:H7 EDL933 NC_007414=92077,NC_002655=5528445
eschColi_O157H7 Escherichia coli O157:H7 EDL933 NC_007414=92077,NC_002655=5528445
eschColi_TW14359 Escherichia coli TW14359 chr=5528136,plasmid_pO157=94601

Public instance

A public instance of Galaxy maintained by Penn State University is at http://usegalaxy.org/

Support

In order to facilitate interaction among UAB Galaxy users, share experience, and provide peer-support we have established a galaxy-user group. To join this group and participate in email discussions please subscribe to the galaxy-user group. On-line archives of these discussions are available here. In addition to the galaxy-user mailing list, we have a galaxy-annce mailing list for UAB's galaxy instance related announcements. The galaxy-annce is a low volume mailing list for announcing service status and system updates etc. Please note, the email discussions are a public forum. You are advised to only post information you are authorized to share and comfortable with being public.

References

Personal tools
Namespaces

Variants
Actions
Navigation
Toolbox