IGV - include new genomes in TSD

Loading genomes

IGV is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.

https://www.broadinstitute.org/igv/

We have developed the following procedure to include new genomes with the IGV inside TSD. The challenge here is to download and process the genome outside TSD (from an internet connected machine) and then transfer this to the TSD. 

Linux

Use genomes already available inside TSD

1. We have included some genomes inside TSD and can be found in the following location.

/shared/bioinformatics/reference-data/

For example HG38 is found in:

/shared/bioinformatics/reference-data/hg38/IGV-files/hg38.genome

2 . Start IGV

  The following is a screenshot showing how to start IGV (example shown is for the project p11). Please note you need to login to the submit host for your project with "-Y" as shown below.

3. Use: genomes -> Load genomes from file to load the .genome file. from the above location

If the genome does not appear in the menu then you need to check whether the following entry is available in the file (after closing IGV)

$HOME/igv/genomes/user-defined-genomes.txt
(If you do not see this file check the preferences to see where it is)

Hg38<TAB>/shared/bioinformatics/reference-data/b38/IGV-files/human_b38.genome<TAB>hg38

Add your own genome

It is assumed that you are aware of how to process new genomes, and if it is not the case please refer the IGV documentation on this (http://www.broadinstitute.org/software/igv/NewGenomeMgmt).

1. Transfer the following files to TSD (

• XX.fa
• XX.genome
• XX.fa.fai 

For example for the genome Hg38

• hg38.fa
• hg38.genome
• hg38.fa.fai 

2. Copy it to the IGV genome directory

(e.g. $HOME/igv/genomes/hg38/)

3. Edit the .genome content

3.1. unzip .genome (Uncompress the files)

3.2. rm .genome (remove the original)

3.3. Edit the property.txt file to include the current sequence location.

i.e. sequenceLocation= $HOME/igv/genomes/hg38/

3.3. Re-compress the .genome file

      zip hg38.genome *

3.4. Load the genome as described in the Use genomes already available inside TSD section.

Expand the application memory

To expand the memory to e.g. 20G please use run the application with the following arguments:

$ ssh -Y pXX-submit
$ module load igv/2.5.3
$ cd /cluster/software/igv/2.5.3
$ java --module-path=lib -Xmx20g @igv.args --module=org.igv/org.broad.igv.ui.Main

Windows

IGV is currently not available for Windows in TSD. Please use the above mentioned Linux version.