Integrated Genome Browser QuickLoad Site

Welcome to the Integrated Genome Browser QuickLoad site, hosted at the University of North Carolina at Charlotte.

The data available via this site are configured for visualization in the Integrated Genome Browser.

Please contact Ann Loraine (aloraine -- at --- uncc.edu) if you have suggestions, questions, or corrections.

 Name                           Last modified      Size  Description
 Parent Directory                                    -   
 A_lyrata_Apr_2011/             13-Oct-2011 13:22    -   Arabidopsis lyrata
 A_thaliana_Apr_2008/           13-Oct-2011 13:23    -   Arabidopsis thaliana
 A_thaliana_Jan_2004/           13-Oct-2011 13:24    -   Arabidopsis thaliana
 A_thaliana_Jun_2009/           15-Feb-2012 11:36    -   Arabidopsis thaliana TAIR9, TAIR10 genome assembly
 B_distachyon_Aug_2010/         13-Oct-2011 13:25    -   Brachypodium (a model grass)
 C_albicans_SC5314_Nov_2008/    07-Dec-2011 12:31    -   Candida albicans
 C_albicans_WO-1_Jul_2010/      07-Dec-2011 09:18    -   Candida albicans
 C_papaya_Aug_2010/             13-Oct-2011 13:25    -   Papaya
 C_reinhardtii_Nov_2010/        13-Oct-2011 13:25    -   Chlamy (an algal genome)
 D_discoideum_Ax4_May_2009/     13-Oct-2011 13:25    -   Slime mold
 G_max_Aug_2010/                13-Oct-2011 13:26    -   Soybean
 M_truncatula_Mar_2009/         21-Oct-2011 20:12    -   Medicago truncatula
 O_sativa_japonica_Jun_2009/    17-Feb-2012 14:00    -   Rice, japonic variety
 P_patens_Jan_2008/             13-Oct-2011 13:26    -   Physcomitrella patens (moss)
 P_persica_Apr_2010/            11-Nov-2011 10:39    -   Peach v1 genome assembly
 P_trichocarpa_Jan_2010/        13-Oct-2011 13:26    -   Black cottonwood (poplar)
 R_communis_May_2008/           11-Nov-2011 17:36    -   Castor bean
 S_bicolor_Jan_2009/            13-Apr-2012 07:25    -   Sorghum bicolor
 S_cerevisiae_Apr_2011/         03-Nov-2011 15:49    -   Budding yeast
 S_pombe_Aug_2007/              13-Oct-2011 13:27    -   Fission yeast
 T_kodakaraensis_KOD1_May_2004/ 08-May-2012 21:44    -   Thermococcus kodakaraensis
 V_carteri_Jul_2010/            13-Oct-2011 13:27    -   Volvox
 V_vinifera_Mar_2010/           13-Oct-2011 13:28    -   Wine grape 12x assembly
 X_tropicalis_Nov_2009/         27-Apr-2012 16:42    -   Xenopus tropicalis JGI 4.2/xenTro3
 Z_mays_B73_Mar_2009/           13-Oct-2011 13:28    -   Zea mays B73 AGPv1 assembly
 Z_mays_B73_Mar_2010/           26-Oct-2011 02:00    -   Zea mays B73 RefGen_v2 assembly
 contents.txt                   08-May-2012 21:37  1.4K  Available genome assemblies and their titles
 favicon.ico                    17-Apr-2011 11:52  7.1K  Icon IGB displays for this data source in the Data Access tab

About QuickLoad

A QuickLoad site can be located on the Web or on your local file system. It just needs to contain some basic files describing your genome and follow a simple structure, as follows. Other documentation is located on the IGB wiki: About QuickLoad.

contents.txt: This file lists the genome versions your Quickload will contain. Put this file at the top level of your Quickload directory - the Quickload data root. The first column gives the folder (directory) name for each genome version, and the second column specifies the genome's title that will appear above the data display in IGB. Here is an example. To ensure that IGB will display the latest release first, use the naming convention G_species_mon_yyyy, for example, B_distachyon_Aug_2010, where G is the first letter of the genus, species is the species, month is a three letter abbreviation of the month (English) and yyyy is the year of the release.

genome.txt: This simple file should contain a list of all the chromosomes (or contigs) your finished or partially assembled genome contains. It should have two columns of data, separated by tabs. The first column lists the names of the chromosomes (or contigs), and the second column lists their sizes, in base pairs. For each genome, create a genome.txt file and place it in that genome's subdirectory in your Quickload data root. Here is an example from grape.

favicon.ico: This is a small image file IGB will display next to your data source in the Data Access panel. It is optional. To find out more about favicon.ico (short for favorites icon) read this wikipedia entry.

Genome data directories: Put your annotation and sequence files into subdirectories for each genome version you want to support. The name of the genome data directory should match the first column from your contents.txt file.

annots.xml: Each genome data directory should contain an annots.xml file that lists all the annotation files you want to make available via Quickload. For an example, see the annots.xml file for Zea Mays genome annotations. List each data set using the "file" tag, which should have these attributes:

name - name of the file (e.g., TAIR9_mrna.bed.gz)
title - the data set title, this appears in the Data Access Panel
description - the text for the tooltips IGB will display about the data set [optional]
url - link to a Web page that has more information about the data set [optional]

Annotation data files. Put annotation files for each genome in that genome's data directory. IGB supports many formats. For gene models, use bed, developed by the UCSC Genome Bioinformatics group. Here is an example from maize: Z_mays_B73_Oct_2009.bed.gz. For EST or mRNA alignments, use psl which is the output from Jim Kent's blat alignment tool. For alignments of short read (e.g., Illumina) sequences onto a genome, use sorted, indexed BAM files. Be sure to include a BAI (BAM index) file in the same directory as your BAM file. Note: make sure you set the maximum intron size parameter wisely if you are using blat: plant introns are typically much smaller and the maximum intron size should be set accordingly. Contact Ann Loraine if you have questions about this.

Sequence data files. For sequence, use bnib or 2bit, binary formats that speed up loading sequence data into the viewer. We highly recommend using the 2bit format! You can create a 2bit file very easily using Jim Kent's faToTwoBit program, available from the UCSC Genome Bioinformatics site. To find it, google faToTwoBit.

If you decide to use the recommended 2bit format for distributing sequence data, you must name the 2bit after the genome version directory it resides in. For example, genome version V_vinifera_Mar_2010 2bit file should be named V_vinifera_Mar_2010.2bit.

If you make a 2bit file for your sequence data, you can also use it to create the corresponding genome.txt file. Just get a copy of Jim Kent's twoBitInfo program to create the genome.txt file. And, of course, you can use your genome 2bit file as a target seqeunce for running the Kent spliced alignment tool blat for a quick-and-dirty first pass annotation.

If you choose to use a bnib file instead, you should create a bnib file for each sequence. These should match the names of chromosomes listed in the genome.txt file. For example, if the genome.txt file contains a sequence named contig123, then the corresponding sequence file should be named contig123.bnib.

To create a bnib file, you can use code from the Genoviz project and convert a fasta format file to the binary bnib format. Read the documentation How to create binary sequence files in BNIB format.