introducing BAMseek, a large file viewer for BAM and SAM

[BAMseek]

Hi SeqAnswers community,

I have been a long time follower of SeqAnswers but have just joined and would like to make available a tool I have been working on called BAMseek.

BAMseek is a large file viewer for browsing BAM and SAM alignment files. BAMseek offers a graphical interface to viewing SAM/BAM files and allows you to jump around to random locations in your files.

I currently have a Mac OS X Snow Leopard build available at http://code.google.com/p/bamseek/ If people find this useful, I can also make a Windows executable available.

This is the first release of BAMseek, so any suggestions/feedback/questions are welcomed. I will do my best to reply and incorporate feedback.

thanks!

[zee]

Does it have the ability to non-interactively generate "snapshots" of a given region of the fly? Im looking for this in an open source tool.

[dp05yk]

I found it easy to install, and it is a very clean interface.

[BAMseek]

Does it have the ability to non-interactively generate "snapshots" of a given region of the fly? Im looking for this in an open source tool.

Hi zee,
I don't know if I quite understand what you mean. I could add the ability for the user to select a few rows and do a Copy of the selected data (in fact, I think that would be nice for the next version). If you are looking to automatically extract all the reads in a certain genomic region, I would suggest the "samtools view" command in the samtools software (which requires the file to be sorted and indexed). For BAMseek, I decided to not require the file to be sorted in order to browse it.

Does that help at all?

[tnabtaf]

Can you summarize how BAMseek compares to other BAM viewers like Bambino and BamView? What are it's relative strengths?

Thanks

[BAMseek]

Can you summarize how BAMseek compares to other BAM viewers like Bambino and BamView? What are it's relative strengths?

Thanks

Sure. I am aware of the tools you mentioned, but I have not used them too much myself, so please correct me if I am wrong. It looks like those types of programs are for visualizing alignments on the genome, which is a very useful way for exploring your data. BAMseek gives you a different view of the data - it allows you to view the file itself, which to my knowledge, could only be done if you are familiar with command line operations. Typical text editors cannot view SAM/BAM files because the files are large (too much to put into memory at once), and BAM files are not in a human-readable form. BAMseek could be useful if you just wanted to open up the file and get a feel for the type of data it contains - is it paired-end? does it contain auxiliary flags? what's the read length? ...

So in short, I see these as complimentary tools that allow you to explore those very large BAM/SAM files.

[zee]

OK I had a look at Bamseek and I thought it would be another alignment graphical viewer. It definitely does not suit my purposes as I am already quite experienced with the samtools and Picard utilities. Nice for the GUI people though.

[BAMseek]

BAMseek - now on Windows

Cross-platform version of BAMseek now available at

http://code.google.com/p/bamseek/

BAMseek is a file viewer that allows you to browse through BAM and SAM files with a friendly user interface. I recently uploaded a cross-platform version (BAMseek2011June01.jar ) that can run on both Windows and Mac (and anywhere java runtime 1.6 is installed). To run, simply download and double click the .jar file. I would still consider this in its testing stage, so keep that feedback coming! Thanks.

[narain]

How different is it from IGC and TVIEW ? I know IGV changes the BAM alignment of my reads to reference , and so I have discontinued using it. I hope BAMseek does not do the same.

[BAMseek]

BAMseek is a text viewer that lets you see the actual text within a BAM file (such as what you would get with samtools view). So probably not what you are looking for if you are looking for a new alignment viewer. What do you mean that IGV changes the BAM alignments to reference? I haven't noticed IGV changing the data.

Justin

[madebeljak]

Hi,

I have tried BAMSeek and like the way it gives individual reads; however, it seems that is all there is. Is there a "search/find" function if I wanted to look for a specific sequence. Or is there a freely available tool for this?

Thanks,
Marija

[BAMseek]

Hi,

I have tried BAMSeek and like the way it gives individual reads; however, it seems that is all there is. Is there a "search/find" function if I wanted to look for a specific sequence. Or is there a freely available tool for this?

Thanks,
Marija

You are correct, there isn't a search/find function available. To do that, there is a lot of power and flexibility from using samtools and grep in the command line. You might try something like this

samtools view -h input.bam | grep TCTGACTCTGTGTA

You can get fancy and limit your search to particular columns (using something like awk) or allow for mismatches in the sequence using wildcards. So I would suggest that route. Hope that helps.

Justin