MagicViewer: Next-generation Sequencing Data Visualization and Variation Annotation

[houhuabin]

To satisfy the impending need for deciphering the large-scale data generated from next-generation sequencing, a sophisticated software MagicViewer is developed to easily visualize the short reads alignment, identify the genetic variation and associate with the annotation information of reference genome. MagicViewer provides a user-friendly interface in which large-scale short reads and sequencing depth can be easily visualized in zoomable images under user definable color scheme through an operating system-independent manner with the implement of Java language. Meanwhile, it holds a versatile genetic variation annotation and visualization interface, providing details of the query options, functional classifications, subset selection, sequence association and primer design.

Highlights of MagicViewer:

· Provided a user-friendly interface with memory efficient to display large-scale short reads, obtaining from high-throughput sequencing.

· Powerful visualization property for graphical visualization of genetic variation and associated annotation information.

· Flexible customizable configure supports zooming, font and colors definition schemes.

· Employed the SAM format instead of native format to compact with other software with respect to input/output data format.

· Different visualization section is design as tracks, allowing adding, deleting and rearranging.

· Written in Java programming language and can be performed in an operating system-independent manner for which a Java virtual machine is available.

· Introduced the workspace where users can easy create new project, save the intermediate result.


MagicViewer can be accessed at http://bioinformatics.zj.cn/magicviewer/.

[tsucheta]

Hi,

I am looking for a viewer as described by you. However, my shortcomings are the bam files are around 6 GB long and I am not sure if my windows machine will be able to handle this. Another question I have is, can I make it web enabled, so that users can browse this through our web server.

Many thanks

Sucheta

[houhuabin]

Hi Sucheta ,

During our evaluation, MagicViewer worked properly with the bam files of 4 GB size under 2GB RAM. You can have a try for your 6 GB size of bam file on your own computer.

The web-based version of MagicViewer (Java applet for use in web applications) is still under development. We hope it to be finished in 2-3 months.


Given MagicViewer 1.1 is in its early days, you may meet some potential bugs. Please don't hesitate to contact us if you have any questions.

Thanks!

[broadIT]

IGV is a high-performance visualization tool for interactive exploration of large, integrated datasets. Of course, it can visualize diverse next-generation sequencing datasets.

IGV is available at http://www.broadinstitute.org/igv/?q=home

[houhuabin]

I found that many java codes in your MagicViewer take from Integrative Genomics Viewer (IGV) software of Broad Institute of MIT and Harvard.

However, you did'nt mention and cite IGV software in your MagicViewer and your website.

IGV is a high-performance visualization tool for interactive exploration of large, integrated datasets. Of course, it can visualize diverse next-generation sequencing datasets.

IGV is available at http://www.broadinstitute.org/igv/?q=home

Dear broadIT,

We have not taken codes from the IGV software. However, we have referred the codes from inGAP (inGAP: an integrated next-generation genome analysis pipeline. Bioinformatics. 2010 Jan 1;26(1):127-9). Now, we are comparing the codes.

Thank you for your reminder. If it is the fact, we will cite the IGV software. Thank you for your suggestion.

[houhuabin]

Dear broadIT,

We found that there are several java classes, which are assigned the same names between MagicViewer and IGV, such as AlignmentTrack, DataSource, Track, TrackSet and SamUtils. However, the codes content and style within the classes are different. Can you attach some codes that you consider to take from IGV here? We will check them carefully.

Thank you again for boring you so much!

[broadIT]

in your lib directory. some binary codes is the same IGV. You can compare them.

[houhuabin]

Dear broadIT,

We have checked our MagicViewer tool carefully. In our lib directory, there are five JAR files as the same to IGV. There are AbsoluteLayout.jar, colt.jar, junit-4.5.jar, sam-1.08.jar, swing-layout-1.0.jar. Beside the sam-1.08.jar taken from Picard (Picard is Java-based utilities of SAMtools, MagicViewer implemented the Picard to manipulate the SAM files), the other four JAR files are all the common libraries for Java language. Other specific JAR files are from GATK.

We do not known which codes you indicated to take from IGV. Can you give the cases?

[broadIT]

There are no documents about the sam-1.08 take from where in your MagicView and IGV. So, I think you take sam-1.08 from IGV. You should provide details about their source and acknowledgement in your software. Thanks for your reply!

[houhuabin]

Dear broadIT,

Now, the misunderstanding has been resolved. Thank you for your suggestion. If you have any question, please do not hesitate to contact us, which will be an important step for enhancing the power of MagicViewer and our future update. We expected that MagicViewer can serve as a powerful short reads visualization and genetic variation annotation tool for next-generation sequencing data

[biofqzhao]

Here are two of them.
it can only recognize "*.fa" and ".fasta" formats as the default. But sometimes users may have a different extension name ".fna" or "faa". So you may fix it.

$ java -mx2000m -jar MagicViewer.jar
Exception in thread "Thread-6" java.lang.IllegalArgumentException: File is not a supported reference file type: /Volumes/NewSolexa/WgsMapping2/newref.fna
at net.sf.picard.reference.ReferenceSequenceFileFactory.getReferenceSequenceFile(ReferenceSequenceFileFactory.java:72)
at net.sf.picard.sam.CreateSequenceDictionary.makeSequenceDictionary(CreateSequenceDictionary.java:139)
at net.sf.picard.sam.CreateSequenceDictionary.doWork(CreateSequenceDictionary.java:124)
at utils.SamViewUtil.createSequenceDictionary(SamViewUtil.java:43)
at Magic.Units.File.FastaFile.generateDicAndIndex(FastaFile.java:59)
at utils.SamViewUtil.processAlignmentFile(SamViewUtil.java:58)
at Magic.WinMain.NewBAMJDialog$8.construct(NewBAMJDialog.java:365)
at Magic.Units.Gui.SwingWorker$2.run(SwingWorker.java:115)
at java.lang.Thread.run(Thread.java:637)

Then I renamed the reference.
$ mv /Volumes/NewSolexa/WgsMapping2/newref.fna /Volumes/NewSolexa/WgsMapping2/newref.fa

Another problem came out. It seems that samtools did not work functionally in my mac desktop. But actually, when I used the stand-alone version, it works very well.

$ java -mx2000m -jar MagicViewer.jar
samtools faidx "/Volumes/NewSolexa/WgsMapping2/newref.fa"===========================
samtools faidx "/Volumes/NewSolexa/WgsMapping2/newref.fa"===========================
Exception in thread "Thread-6" net.sf.picard.PicardException: Unable to load fasta index file /Volumes/NewSolexa/WgsMapping2/newref.fa.fai. Please create it using 'samtools faidx'.
at org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile.loadIndex(IndexedFastaSequenceFile.java:119)
at org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile.<init>(IndexedFastaSequenceFile.java:63)
at Magic.Units.Main.ViewerLog.setViewerLog(ViewerLog.java:52)
at Magic.WinMain.NewBAMJDialog$8.construct(NewBAMJDialog.java:368)
at Magic.Units.Gui.SwingWorker$2.run(SwingWorker.java:115)
at java.lang.Thread.run(Thread.java:637)

[houhuabin]

Dear zhao,

Sorry for inform you so late.
The MagicViewer can now surport suffix of "fna" and "faa" in the lastest version, and we have solved the bugs of index fasta file in mac, after regression testing we will release in the next version.

Thanks!

[byb121]

Dear huabin,

I just tried magicviewer, I would say it's an easy to use software with beautiful interface, nice work!
It runs smoothly in windows, but there is a flaw (probably my fault as I am a new linux user) in Linux, the same files that worked fine in windows couldn't be loaded in my Ubuntu system.

$sudo sh MagicViewer.sh
java.io.FileNotFoundException: /transcriptsData/GSE11209/ana/magicviewer/SRX000559.SRR002051.map.sorted.bam.bai (No such file or directory)
	at java.io.FileInputStream.open(Native Method)
	at java.io.FileInputStream.<init>(FileInputStream.java:106)
	at java.io.FileInputStream.<init>(FileInputStream.java:66)
	at utils.Remove0D.remove(Remove0D.java:28)
	at utils.SamViewUtil.rm0d(SamViewUtil.java:116)
	at utils.SamViewUtil.processAlignmentFile(SamViewUtil.java:102)
	at Magic.WinMain.NewBAMJDialog$8.construct(NewBAMJDialog.java:351)
	at Magic.Units.Gui.SwingWorker$2.run(SwingWorker.java:115)
	at java.lang.Thread.run(Thread.java:619)
Exception in thread "Thread-9" net.sf.picard.PicardException: Unable to load fasta index file /transcriptsData/GSE11209/ana/magicviewer/sacCer.fa.fai.  Please create it using 'samtools faidx'.
	at org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile.loadIndex(IndexedFastaSequenceFile.java:121)
	at org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile.<init>(IndexedFastaSequenceFile.java:60)
	at Magic.Units.Main.ViewerLog.setViewerLog(ViewerLog.java:52)
	at Magic.WinMain.NewBAMJDialog$8.construct(NewBAMJDialog.java:354)
	at Magic.Units.Gui.SwingWorker$2.run(SwingWorker.java:115)
	at java.lang.Thread.run(Thread.java:619)

My java is fine (at least I believe so).

$ java -version
java version "1.6.0_15"
Java(TM) SE Runtime Environment (build 1.6.0_15-b03)
Java HotSpot(TM) 64-Bit Server VM (build 14.1-b02, mixed mode)

Any suggestion to get around with it?
Thanks

[houhuabin]

Dear byb121,

Thanks for using MagicViewer!
Could you tell me whether your computer is linux 32 or 64 bit?

Huabin

[houhuabin]

Hi,

The new version of MagicViewer(Ver. 1.1.5 ) have released now.
The bugs reported by zhao and byb121 have fixed. You can try it now, If you have any questions, please don't hesitate to contact us.

Thanks

Huabin