BAMseek

{{Bioinformatics application |sw summary=BAMseek is a large file viewer for BAM and SAM alignment files. |bio domain=Alignment, |bio method=Alignment viewer, |bio tech=All, |created by=BAMseek |created at=Backyard deck. |maintained=Yes |input format=SAM/BAM, |output format=None |language=C++, Qt4 library, |licence=GPLv3, |os=Mac OS X 10.6, }}

BAMseek

A Large File Viewer for BAM and SAM alignment files.

What is it?

BAM and SAM alignment files are usually large and cannot be easily opened in common text viewers. BAM files are not human-readable so need a specialized viewer to interpret the information contained within the files. BAMseek allows you to open and browse SAM and BAM alignment files, no matter how large the files may be. BAMseek does not require command line knowledge. Instead, BAMseek provides a comfortable point-and-click interface for browsing BAM and SAM files.

How do I install it?

Download the BAMseek application here. The latest version is 0.1.3. Currently, BAMseek is only available for *Mac Os 10.6 (Snow Leopard)*, but the Windows version is in the works. Open the DMG and drag the application to any location on your computer (such as your Applications folder). Open the BAMseek application by double-clicking it, or by double-clicking one of your SAM or BAM files.

How do I use it?

After opening BAMseek, if you do not already have a file open, go to File > Open... Browse to the location of a SAM (.sam) or BAM (.bam) file and select it. If the file is large, it may take a little while for the file to be processed and opened. For the impatient, you can cancel a file load that is in progress, and you will be able to view the file up until the point you canceled the progress.

The advantage of BAMseek is that you can browse the entire file and only use a small amount of memory, even for large files. The file is divided into pages, with each page having a length of 1000 lines. You can browse within a page by using the scroll bars or mouse wheel. You can jump between pages using the slider and scroll box at the bottom of BAMseek.

What other cool things can I do with BAMseek?

Here are some of the features currently in BAMseek The header information is stored at the top of the BAMseek window. You can move the header in and out of the main window by going to File>Dock/Undock Header.

Are you confused by the Cigar or Quality Score columns?  Hover over cells to get more information about the item in the cell.  Currently, you can 
 hover over Flag (Column 2) to translate the meaning of the flag description.
 hover over Cigar (Column 6) to understand how the read was aligned to the sequence.
 hover over Sequence (Column 10) to see which bases are high quality and which are low quality.  A base is grayed out if the Phred quality is below Q20 (more than  a 1 in a 100 chance of being an incorrect base call). 

Really? BAMseek can view files larger than the memory capacity? What kind of black magic is this!?

BAMseek groups the BAM or SAM file into pages, and only loads the currently viewed page into memory - similar to how you view a large book one page at a time. The disk address of each page is computed when you open the file, allowing you to quickly jump to any page you want.

So who are you?

My name is Justin, and I am a software developer working for the past 3 years on analyzing Next-Generation Sequencing data. I wanted to do something to give back to the community, so I spent some nights and weekends putting this together in hopes that others will find it useful. Please let me know if you have feedback (both positive and negative), questions, or suggestions. I will continue to update the software so check back often. Thanks!

Links

• BAMseek Binaries [ edit link ]
• BAMseek Source code [ edit link ]

• Add a Link

References

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