Installation and system requirements

System requirements
Java 1.6u10+ is required to run the application. You can get a recent version from http://www.java.com. It is recommended that you have 1 Gb of memory, but GenomeView will work with less. Similarly it is recommended to have a dual-core or better processor, but GenomeView will work with less.

Installation
The most straightforward way to start GenomeView is by Java Webstart.

Clicking the above button will immediately launch the application.

Local installation
You can download the latest version from http://sourceforge.net/projects/genomeview/

Unpack the zip file to a directory and start the genomeview-.jar file. You can start this file either by double clicking the jar file or by issuing the following instruction at the command line.
java -Xmx1g -jar genomeview-<version>.jar,
where <version> is replaced by the appropriate version number.

Supported platforms

This is a compatibility matrix of GenomeView with various OS/browser combinations. The Web Start version matrix only has the operating system as it is independent of the browser. The Applet version of GenomeView has many more combinations, not all of which work equally well.

The green means we have confirmed this combination to work. A red means we could not get it to work. Blanks in the table are combinations we haven't been able to test, your help is appreciated in filling the blanks.

GenomeView requires at least Java 1.6u10. This is a higher version than by default available on some platforms. In those cases you need to update Java first.

Webstart version

Only major names are included as we have not yet received reports of any recent unsupported versions or minor versions. If you come across any, please let us know.

Operating System	Status
Windows
Linux
OS X

Applet version

There is a table per operating system as there are typically many flavors of each OS. If a version is missing, feel free to contact us and we'll add it. We try only to include major versions, but if some minor versions behave differently they will be included. For example Firefox 3.6.14 broke applet support completely.

Windows

	Windows XP	Windows Vista	Windows 7
Firefox 3.6.15+
Firefox 4
Firefox 5
Firefox 6
Firefox 7
Firefox 8
Chrome 12
Chrome 13
Internet Explorer 7
Internet Explorer 8
Internet Explorer 9
Safari 5.0
Safari 5.1
Opera 11

Linux

	Ubuntu 10.04 Lucid Lynx	Ubuntu 11.04 Natty Narwhal
Firefox 3.6.15+
Firefox 4
Firefox 5
Chrome 12
Chrome 13
Internet Explorer 7
Internet Explorer 8
Internet Explorer 9
Safari 5
Opera 11

Mac OS X

	OS X 10.5.8 Leopard	OS X 10.6.8 Snow Leopard	OS X 10.7 Lion
Firefox 3.6.15+
Firefox 4		*
Firefox 5		*
Chrome 12		*
Chrome 13		*
Internet Explorer 7
Internet Explorer 8
Internet Explorer 9
Safari 5.0
Safari 5.1		*
Opera 11

^*On Mac OS X, some browsers need a work-around to get the applet visible:

1. Wait for GenomeView to load, even if it is blank
2. Press CMD+Shift, en keep it pressed
3. At the top of the applet there appears a bar
4. Click the bar (you can now release CMD+Shift) and drag it outside the browser

Your assistance needed!

We need help to fill in the blanks.

To test the applet please go to http://genomeview.org/start/applet.html. If it starts GenomeView, you can load data from one of the demo instances and it shows the data. The GenomeView applet works on that OS/browser combination.

Send your experiences to support@genomeview.org and they will be included in the table.

Make sure you provide detailed version information for both the browser you tested and your operating system as well as your exact Java version.

If your experiences do not match with the table, let us know and we'll investigate further.

For Mac OS X testers: if the regular test fails, please test the following work-around and report those results as well:
Press CMD+Shift and the top bar of the applet appears in the browser. Drag the applet out of the browser. It should now paint correctly.

List of testers

Your name will appear here if you contribute to the compatibility matrix
Peter Sisk
Jon Goldberg
Ken Heyndrickx
Bram Verhelst
Michiel Van Bel

Navigation

Navigation can either be done with the buttons in the toolbar (arrows and magnifying glasses), with the navigator panel (ruler at the top with a block box), with the mouse or with your keyboard.

Navigator
Drag the edges to zoom in/out. Cursor will change to a resize icon when you are at an edge. Drag the box or the half-circle handles to move to another place in the genome. Click somewhere on the ruler to move to that place.

Mouse

Ctrl+scroll wheel

Zooming

Scroll wheel

Scroll through tracks

Drag left-right

Move left-right

Shift+ drag left-right

Select sequence

Keyboard

+/- keys

Zooming

Arrow keys left-right

Move left-right.

Load data

Sources
You can load data from files from your computer, or you can load data from a file that lives on the internet by its URL.

File formats
GenomeView supports a whole list of file formats. See the data format page for a complete list. GenomeView tries to limit the listed files to the supported data formats. However, there are many extensions in use and your files may be hidden. In that case, select "all files" from the drop-down list.

Some file formats can/need to be preprocessed for optimal performance.

• Preparing fasta files
• Preparing read mapping (SAM/BAM) files
• Preparing pile-up (read coverage plots)

Opening a file
Steps to open a file:
File > Load data > Local file > pick your file

Note that you can select multiple files at once.

There are two sample data files attached to this page you could use. One file contains genomic sequence, the other one annotation for this sequence. The data represents the mitochondrial DNA of C. elegans (WS200).

The video's below show how to open data from a local file and from a URL.

Watch the video full screen for best quality

Watch the video full screen for best quality
Loading data from a URL

Attachment	Size
CHROMOSOME_MtDNA.fasta	13.75 KB
MtDNA.gff	3.35 KB

Data formats

Currently several commonly used formats are recognized by GenomeView. GenomeView using the identifiers present in each format to link different sources, so make sure that the identifiers match (case-sensitive).

Make sure you index your large files: reference genome, NGS data sets (SAM / BAM), annotation and read coverage plots While this is not required, it will speed up the process of browsing and loading data, as well as significantly reduce the amount of memory you need.

Input formats

Data type	File format	Index*	Max size**		Comments
			unindexed***	indexed
Reference sequence	fasta ¤	Recommended	50 Mb	unlimited	GenomeView will automagically create index for you if you don't have one.
	embl, genbank	Not possible	50 Mb	--	EMBL and genbank are mixed file formats that can contain both annotation and reference sequence at the same time.
Annotation	gff ¤	Not recommended	50 Mb	unlimited
	embl, genbank	Not possible	50 Mb	--	EMBL and genbank are mixed file formats that can contain both annotation and reference sequence at the same time.
	bed	Not possible	50 Mb or less	--	By default data from a bed file is added to the CDS track, if you want it in a different track, you have to add a line a the top of the file 'track name=Track_name'. No white-space is allowed in the track name.
	ptt, tbl	Not possible	50 Mb or less	--	Other standard annotation formats GenomeView understands
various formats	Not possible	50 Mb or less	--	GenomeView can directly parse the output of the following programs: Blast, GeneMark, TransTermHP, FindPeaks, MaqSNP, tRNA-scan
Multiple genome alignment	maf ¤	Recommended	100 Mb	unlimited	GenomeView will prompt you to create a compressed maf file and index it for you, if you're trying to load an unindexed maf file. MAF is the recommended file format for whole genome alignemnt of large/complex genomes
	multi-fasta ¤	Not possible	100 Mb	--	Recommended for small/simple genomes with a near 1:1 relationship.
	aln, ClustalW	Not possible	100 Mb	--
Sequence read alignment	bam ¤	Required	--	unlimited	GenomeView will prompt you if there is no index and will create one for you.
	MAQ, MapView, BroadSolexa	Not possible	100 Mb	--
Read coverage summary	tdf ¤	Native	unlimited	unlimited	TDF files can be created with the tdformat tool that is available for download.
	bigwig	Native	unlimited	unlimited	This format can be used for any wig file, not just read coverage
	pileup	Required	--	unlimited	The pileup format becomes slow when you have extreme read depth (>5000 x coverage)
	wig	Not possible	50 Mb	--	We strongly recommend to convert your wig files to bigwig or TDF. GenomeView can automatically convert wig files to TDF. Caveats: 'track' information should all be on a single line, 'browser' lines will be ignored as the are specific to the UCSC Genome Browser. WIG files need to be sorted by chromosome and by genomic coordinate within the chromosome. BedGraph as well as Wiggle_0 format is supported. For the wiggle_0 type, both variableStep and fixedStep should work.
Allele diversity summary	pileup ¤	Required	--	unlimited	The pileup format becomes slow when you have extreme read depth (>5000 x coverage)

* Indicates whether this file format can/should be indexed.

** Recommended maximum file size. First value is without index, the second with index. This values are only guidelines. When loading multiple data sets, you should add the sizes.

*** Unindexed data files can be gzip compressed.

^¤ Recommended file format for this data type.

Output formats

(Modified) annotations can be saved as either GFF or EMBL.

All data that is loaded can be exported in their original format. This will not include modifications.

Preparing fasta files

To be able to easily handle large vertebrate reference genomes, it is required that they are indexed. This can be done with the faidx command from the samtools package.

If you are also preparing HTS data sets in the BAM format, this step will also be part of that procedure, so either you move right to the short read preparation page or you can skip the step there whenever you're ready.

To index a fasta file you run

samtools faidx reference.fasta


Attention
If your files was reference.fasta, GenomeView will search for reference.fasta.fai in the same directory. If you want to be able to load large files, make sure those two files are correctly named and in the same folder.

You can download the samtools package from Sourceforge.

Preparing feature files

Large feature files need to be indexed before you can use them properly in GenomeView.

The definition of large is not strict in the sense that it depends on both the real size of the file, as well as the number of features in the file.

Recommendations:

• Only index feature files that are larger than 5 Mb or even 10 Mb when compressed with GZIP.
• Only index feature files that do contain composite features, i.e. feature consisting of multiple locations. The prime example are eukaryote genes.
• Typically the annotation of a genome does not need to be indexed if it just contains genes, mRNA, CDS and exons

Instructions:
To index a file, you need to pre-process it with tabix, much like is done with pile-up files.

Tabix can be downloaded from the tabix download page.

For BED formatted files:

sort -k1,1 -k2,2n input.bed | bgzip -c > compressed.bed.gz
tabix -p bed compressed.bed.gz


Note that indexing will not work with BED files that have a UCSC header ("track name=blah")

For GFF formatted files:

sort -T /group/tmp -k1,1 -k4,4n input.gff | bgzip -c > compressed.gff.gz
tabix -p gff compressed.gff.gz


In both cases, you will get two new files: (1) a gz file and (2) a tbi file.
Load the gz file in GenomeView.

Caveat:
The structure of genes will be lost when indexing gff files.

Preparing short read alignments

The best format to present short read alignments to GenomeView is the SAM/BAM format, which is emerging as the standard.

There are a number of tools available to convert the output from numerous aligners to SAM on the SAMtools website.

Once you have a SAM file you need to convert it to BAM and index it. Let us suppose you have a reference sequence called 'reference.fasta' and a read alignment in SAM format called 'alignment.sam'.

Steps to get from the various aligner formats to the SAM format are available on the SAMtools website.

Steps to go from SAM to indexed BAM.

samtools faidx reference.fasta (will create reference.fasta.fai for the next step)

samtools view -bS -t reference.fasta.fai alignment.sam -o alignment.bam

samtools sort alignment.bam sorted (will create sorted.bam)

samtools index sorted.bam (will create sorted.bam.bai, which is read by GenomeView together with the bam file)

Preparing pileup

If you are looking for assistance to load your BAM file, see the short read alignment preparation page

Please see the description of the pile-up track for more information on what can be done with the pile-up track.

There are three formats supported for pileups. The first one is generated with a specific tool that is available from this page. The second one can be generated by samtools, the final one is a simple tab delimited file format. All are explained below, links to samtools and tabix can be found at the bottom of this page.

Important: TDF should not be indexed. The samtools pileup and tab delimited format MUST be indexed before GenomeView understands them.

TDF coverage plot (recommended, coverage only)

TDF is a tiled data format which contains the coverage plot, as well as multiple resolution summaries which allows fast retrieval at any scale.

Download the latest version of tdformat, a small program to generate TDF files from BAM files. The BAM file has to be indexed, i.e. there has to be a BAI file as well.

Once you've downloaded and extracted the program (you need at least the lib folder and the tdformat jar file) you can invoke it with the following commands:

java -Xmx1g -jar tdformat-1576.jar <path to your BAM file>

Replace 1576 with the version number of the file you downloaded.

For large genomes, mammalian genomes for example, you may need to increase the memory allotment for the program:

java -Xmx4g -jar tdformat-1523.jar <path to your BAM file>


The TDF format does not have to be indexed.

SAMTools pileup (includes diversity information, i.e. SNP track)

Note: file name extension should contain .pileup
The first step to be able to browse a pileup is to generate one from your BAM file.

samtools pileup -f reference.fasta sorted.bam >sorted.pileup

As you run this command, you'll see that the generated file can be huge, even for small BAM files.

To be able to browse it in GenomeView, it needs to be indexed with tabix, a tool that is also available from the SAMtools web page.


sort -k1,1 -k2,2n sorted.pileup | bgzip -c > compressed.pileup.bgz
tabix -s 1 -b 2 -e 2 compressed.pileup.bgz


Tab delimited pileup (extension should contain '.swig')

The file should be organized in four columns.
The first column holds the identifier of the sequence, the second column contains the genomic position, the third column contains the number of reads on the forward strand, the final column contains the number of reads on the reverse strand.

1. Identifier
2. Genomic position (one-based)
3. # forward reads
4. # reverse reads

Example:

chr1 11 46 43
chr1 12 47 50
chr1 13 48 61
chr1 14 53 79

Note that the white-space between the columns are tabs, one tab between each column.

Once you have such a file, you can again index it for faster access and shorter download times.

sort -T . -k1,1 -k2,2n filename | bgzip -c > filename.bgz
tabix -s 1 -b 2 -e 2 filename.bgz


Resources

Download samtools
Download tabix

User interface

This page introduces the different components of GenomeView and explains a number of naming conventions we use throughout the documentation.

Components of GenomeView
The GenomeView GUI is divided into two columns. The left side is a graphical representation of the data, while on the right side you can find additional information, controllers and options in the form of tables.

Visual description of the user interface (click to enlarge)

Plugins

Plugins are the basic extension mechanism to create new functionality for GenomeView, without modifying the core application.

Installing a plugin

• Download the plugin. A list of currently hosted plug-ins is available.
• Typically a plugin is distributed in a zip package. Extract the archive, you only need the jar-file. The rest of the archive may contain other useful information, but the jar-file contains the actual plugin.
• Locate the GenomeView configuration and plugin directory: Locating configuration directory
• Copy the jar-file that you extracted into the plugin subdirectory of the .genomeview directory. You should have run GenomeView at least once for these directories to exist.
• Once you (re)start GenomeView, the newly installed plugin will be available.
• New actions that are made available by the plugin are generally available in the 'Plugin' menu

Places to get data

Demo data

We provide a number of demo instances of GenomeView that come with data preloaded.

Preloaded instances

Furthermore we provide a significant number of pre-loaded GenomeView instances through the Genome Explorer.

Other data

Here is a list of a couple of places where you can find data that may be of interest. This data will generally require some processing to get it into one of the standard file formats.

Reference genomes and annotation

If you would like any of the genomes at UCSC or Ensembl included in the Genome Explorer, drop us an e-mail, we have scripts to automate the download and data massaging.
UCSC Genome Browser downloads
Ensembl downloads

Sequencing data sets

Sequence Read Archive (SRA) is a repository that stores raw sequencing data from next generation of sequencing platforms.
EBI Sequence Read Archive is the European cousin of the SRA.

Whole genome multiple alignments

The UCSC data repository has a large number of whole genome multiple alignments. Look under the heading 'Multiple Alignments' for each species.

Some examples:
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/multiz46way/maf/ hg19 aligned to 45 vertebrates
http://hgdownload.cse.ucsc.edu/goldenPath/hg18/multiz44way/maf/ hg18 aligned to 43 vertebrates
http://hgdownload.cse.ucsc.edu/goldenPath/hg18/multiz28way/maf/ hg18 aligned to 27 vertebrates
http://hgdownload.cse.ucsc.edu/goldenPath/dm2/multiz15way/ dm3 aligned to 14 other insects