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For example, there are two Oryza sativa (rice) subspecies in wide cultivation: japonica and indica.The first published rice genome sequence was from the japonica subspecies. Because an indica genome sequence is now available, we need names that distinguish them. We distinguish the japonica assemblies using prefix O_sativa_japonica and the month and year of release: O_sativa_japonica_Oct_2011. Annotations and sequence data reside in genome version folder O_sativa_japonica_Oct_2011 on the main IGB QuickLoad site - . You can view its contents by visiting http://igbquickload.org/quickload/O_sativa_japonica_Oct_2011clicking here.

There is no limit on the number of "_variety" suffixes you can include, provided the genome version name always ends with MMM_YYYY. By including the month and year in the genome version names, you ensure that IGB will display the latest genome version releases first in the Genome Version menu of the Current Sequence tab.

Before you pick a name, also look at the species.txt file that is packaged with every version of IGB. If your species is listed there, then use the genus and species prefix listed in column three of the file. I

After picking an IGB-friendly name, create a sub-folder named for the genome version within the QuickLoad root directory:

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The second column is optional - it contains text IGB will display on the title bar when you open IGB. View an example contents.txt on IGB QuickLoad: httphttps://igbquickloaddata.bioviz.org/quickload/contents.txt

To create a contents.txt file for your QuickLoad site:

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The first column lists the chromosome names and the second column lists their sizes. IGB uses this file to create the sequence selection table under the Data Access Panel.

Here is an example: httphttps://igbquickloaddata.bioviz.org/quickload/A_thaliana_Jun_2009/genome.txt

Create the genome.txt file from a sequence 2bit file (see below) using the twoBitInfo command-line tool, which is available from http://hgdownload.cse.ucsc.edu/admin/exe/.

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Also note that if you are hosting BAM or CRAM files, the BAM index file index (".bai" or ".crai" file ) needs to reside in the same directory as the BAM or CRAM file. Otherwise, IGB will display an error message when users try to access the data.

For more information about annots.xml format, see: About annots.xml

Add  Add annotation files.

Place your annotation, BAM, CRAM, or graph (bedgraph or bigwig) files into the appropriate genome sub-directories. You can you use any format IGB supports. 

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