Artemis

Artemis is a free genome browser and annotation tool that allows visualisation of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation. Artemis is written in Java, and is available for UNIX, Macintosh and Windows systems. It can read EMBL and GENBANK database entries or sequence in FASTA, indexed FASTA or raw format. Other sequence features can be in EMBL, GENBANK or GFF format. Full information about the latest release of Artemis can be found in the Artemis manual.

The Artemis poster gives an overview of browsing genomes and visualisation of next generation data in Artemis.

Publication

High-throughput sequencing (HTS) technologies have made low-cost sequencing of large numbers of samples commonplace. An explosion in the type, not just number, of sequencing experiments has also taken place including genome re-sequencing, population-scale variation detection, whole transcriptome sequencing and genome-wide analysis of protein-bound nucleic acids.We present Artemis as a tool for integrated visualization and computational analysis of different types of HTS datasets in the context of a reference genome and its corresponding annotation.

If you make use of this software in your research, please cite as:

Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data.
Carver T, Harris SR, Berriman M, Parkhill J and McQuillan JA
Bioinformatics (Oxford, England) 2012;28;4;464-9
PUBMED: 22199388; PMC: 3278759; DOI: 10.1093/bioinformatics/btr703

Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database.
Carver T, Berriman M, Tivey A, Patel C, Böhme U et al.
Bioinformatics (Oxford, England) 2008;24;23;2672-6
PUBMED: 18845581; PMC: 2606163; DOI: 10.1093/bioinformatics/btn529

Viewing and annotating sequence data with Artemis.
Berriman M and Rutherford K
Briefings in bioinformatics 2003;4;2;124-32
PUBMED: 12846394

Artemis: sequence visualization and annotation.
Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream MA and Barrell B
Bioinformatics (Oxford, England) 2000;16;10;944-5 PUBMED: 11120685

Software Availability

The Artemis Software is available under GPL3. The source code can be found on GitHub.

The latest release of Artemis can be downloaded by clicking on the relevant link below:

Or via Bioconda. Simply use:

conda config --add channels bioconda     (to add the bioconda channel)
conda config --add channels conda-forge  (to add the conda-forge channel)
conda install artemis

from the command line, and you’re ready to go (no Java installation required).

For older versions of the software please see the Artemis FTP site

The old v17.0.1 version of the Artemis software required Java version 1.8 to run. All recent releases from v18.0.0 onwards require a minimum of Java 9 and ideally Java 11. This must be installed first. The easiest way to install a non-commercial open source Java version is from AdoptOpenJDK - just select the OpenJDK version and Hotspot options for the relevant platform. See the user manual for further options. A Java installation is not required for the Bioconda or Docker options.

Installation

For UNIX/Linux

Change directory to the directory you wish to install the Artemis software in. We will use ~/ in this example and in the next chapter.

Uncompress and untar the artemis-unix-release-{version}.tar.gz or artemis-unix-release-{version}.zip file. On UNIX the command is:

tar zxf artemis-unix-release-{version}.tar.gz

This will create a directory called ~/artemis which will contain all the files necessary for running Artemis and the other tools.

For MacOSX

For MacOSX users, an artemis-macosx-release-{version}.dmg.gz disk image is provided. Double-click on this file in your Downloads folder to unzip it. Then double-click the unzipped artemis-macosx-release-{version}.dmg to mount the “Artemis_Tools” image and display its contents - the Artemis, ACT, BamView and DNAPlotter applications. These apps can then be dragged to any desired location, for example, your dock or desktop. The download file can be unzipped from the command line using gunzip, if necessary:

gunzip artemis-macosx-release-{version}.dmg.gz

There’s also an artemis-macosx-chado-release-{version}.dmg disk image that will start up Artemis with a Chado connection window displayed, if you wish to work connected to a Chado database in Artemis or ACT. This is installed in exactly the same way.

If you wish to run Artemis from the command line instead, then a script is provided within the app package to do this:

Artemis.app/Contents/art

For Windows

Copy the artemis-windows-release-{version}.zip file to the directory that you wish to install to and then unzip using an application such as WinZip. This should unpack the artemis.jar, act.jar, bamview.jar and dnaplotter.jar application files.

Usage

Running Artemis on UNIX/Linux Systems

The easiest way to run the program is to run the script called art in the Artemis installation directory, like this:

artemis/art

Alternatively you can start Artemis with the name of a sequence file or embl file, eg:

artemis/art artemis/etc/c1215.embl

For other available options use:

artemis/art -help

Running Artemis on Macintosh Systems

On MacOSX machines, Artemis can be started by double clicking on the Artemis icon. To start with a sequence file pre-loaded, simply drag the file on top of the Artemis icon.

You may find that when trying to run the Artemis app for the first time, that you get a security warning window displayed stating that “the application cannot be opened because it is from an unidentified developer” (because the apps are not obtained from the app store). If that’s the case, then just okay the window. Go into your System Preferences via the apple symbol at top left of screen. Then select “Security and Privacy”. You should then see a button called “Open Anyway”, next to some text saying “Artemis was blocked from opening because it is not from an identified developer”. Click on the “Open Anyway” button, which will then display the security warning window again - click the “Open” button on it and Artemis should then start. The application will then open straight away after this, without any further security warnings.

Running Artemis on Windows Systems

Artemis can be started by double clicking on the artemis.jar icon.

Running ACT via Bioconda

The Artemis start script is available in the path, so in a terminal window just use:

art

The User Manual

For additional information please see the Artemis manual and our GitHub page. A PDF version of the manual is also available for download here.

Some notes on Chado access can also be found here.

Contact

For issues encountered with installing the software please contact your local system administrator. For all other issues, please report them to our Github issues page or email artemis-help@sanger.ac.uk.

FAQ

Why does Artemis run out of memory on UNIX or GNU/Linux even though the machine has lots of memory?

The Java Virtual Machine (JVM) on UNIX has a fixed upper limit on the amount of memory that is available for applications, but this limit can be changed at runtime. As shipped Artemis will use a maximum of 2GB of memory.

There are two ways of fixing this problem:

Change the art script. Find the line that reads: FLAGS=”-mx2g -ms100m -noverify” and change the 2g (2 gigabytes) to a bigger number dependent on your machine memory (try 3g), or
Create an ARTEMIS_JVM_FLAGS environment variable set to “-mx2g -ms100m”, adjusting the mx value as required. No script change is required for this, but it would need to be added to your environment.

Why does Artemis run out of memory on MacOSX even though the machine has lots of memory?

To change the memory allocated to Artemis on MacOSX, set the value in the file Info.plist in the directory Artemis.app/Contents. Towards the bottom of the file you will see these lines:

<key>JVMOptions</key>
<array>
<string>-mx2g</string>

Changing the value after -mx will change the max memory used by Artemis. The default is 2Gb.

Why does Artemis run out of memory on Windows even though the machine has lots of memory?

Normally the Java virtual machine artificially limits the amount of memory that Artemis can use. The fix is as follows:

Create a shortcut to the artemis.jar JAR file. Edit the properties of the shortcut and add java -mx2g -jar to the start of the Target: field. -mx2g sets the maximum memory Java will allocate to Artemis (2 gigabytes in this case). We recommend choosing a number that is about 50 megabytes less than the total amount of memory in the machine (to allow for the overhead of windows and the Java virtual machine).

You will need to use the shortcut to run Artemis from then on.

The Artemis Software

The Artemis Software is a set of software tools for genome browsing and annotation