BAMseek

Application data
Created by	BAMseek
Biological application domain(s)	Genomics, Transcriptomics
Principal bioinformatics method(s)	Sequence alignment visualisation
Technology	Any
Created at	Backyard deck.
Maintained?	Yes
Input format(s)	SAM, BAM, VCF
Programming language(s)	Java
Licence	GPLv3
Operating system(s)	Cross-Platform

Summary: BAMseek is a large file viewer for BAM and SAM alignment files.

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BAMseek

A Large File Viewer for BAM and SAM alignment files.

NEWS: June 14, 2011

Added support for FASTQ files. Also, it detects if the FASTQ file was generated by CASAVA 1.8 and expands the header line into machine name, lane, xy coords, etc.

NEWS: June 07, 2011

Added support for Variant Call Format (VCF). BAMseek recognizes uncompressed VCF files and BGZF-compressed files (which is how they are stored in the 1000 genomes project). I would like to add support for Standard Flowgram Format (SFF). Look for that in upcoming releases.

NEWS: June 02, 2011

BAMseek has been updated to now work on Windows. Please check out BAMseek for the latest version.

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. It can also view VCF files and soon be able to view SFF files. The goal is to open and browse some of the common Next-generation sequencing formats that would not be feasible with standard text viewers (such as Notepad or Word).

How do I install it?

Download the BAMseek application here. Download the ".jar" file and double click to open. You may open a SAM/BAM or VCF file by going to File > Open... The program has been tested to work on Mac and Windows. It should work wherever the Java runtime is installed. Let me know if you run into problems installing or using the software.

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), BAM (.bam), or VCF (.vcf or .vcf.gz) 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

• 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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