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For example, A_thaliana_Jun_2009 is the TAIR10 Arabidopsis thaliana genome assembly that was released in June 2009.

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For example, there are two Oryza sativa (rice) subspecies in wide cultivation: japonica and indica.The first rice sequence published was from the Nipponbare variety which is a member of the japonica subspecies. Because an indica genome sequence is now available, and we need names that distinguish them. We designate assemblies of the original japonica genome sequence using prefix O_sativa_japonica and the month and year of release: O_sativa_japonica_Jun_2009. Annotations and sequence data reside in genome version folder O_sativa_japonica_Jun_2009 on the main IGB QuickLoad site - view its contents by visiting http://igbquickload.org/quickload/O_sativa_japonica_Jun_2009

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This file should be plain text, tab-delimited; all columns must be separated by a tab character!. If you create this file by hand, be sure to use a text editor that inserts tab characters when you type a tab.

The first column should list names of the genome directories you have created and want to share.

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This is a list of synonyms for genomes.   This list allows you to match names across diverse quickload sitesdifferent QuickLoad sites and also the Galaxy workflow site. For example, if a DAS1 or DAS2 data source (such as ones hosted at Ensembl or UCSC) QuickLoad site at another location uses different names to refer to the same genome version, you can specify these in the synonyms.txt. Each line contains any number of synonyms for a genome, separated by tabs.  

Here is an example: http://igbquickload.org/quickload/synonyms.txt

Step Four: Create genome.txt files for each genome.

For each genome directory, create a genome.txt (formerly, mod_chromInfo.txt) file that lists all the chromosomes in your genome, together with their sizes.

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This describes how contigs are assembled into chromosomes.  

Each line contains:  CONTIG_START tab CONTIG_NAME tab CONTIG_LENGTH tab CHROMOSOME_NAME tab CHROMOSOME_LENGTH

Note: This is a relatively old feature in IGB and we are not entirely sure it still works.

Step Five: Create annots.xml files.

If you have any annotations for your genomes, you can make it possible for IGB to display them in the Data Access Panel by listing them in the annots.xml file.

Here is an example:

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Each genome version subdirectory needs an annots.xml file that is either empty or contains a listing of annotations you want to appear the Available Data Sets section of IGB's Data Access tabbed panel.

Here is a simple example:

<files>
  <file name="TAIR10.bed.gz" 
   title="TAIR10 ALL" 
   description="All TAIR10 genome models" 
   label_field="id"

   background="000000"
   foreground="00FFFF"
   max_depth="10"
   name_size="12"

/>

</files>

Note that the name attribute of the file tag indicates the physical location of the file relative to the directory where the annots.xml file resides. However, you can also use a URL to indicate the location of the file. This means that you if you want to reference other resources hosted on other machines, you can do it.

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

When loaded into IGB, each file will create one or more tracks. (Some file types, such as BED and GFF3, can specify multiple tracks.)

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