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Old 08-12-2009, 12:12 AM   #1
Junior Member
Location: Sydney

Join Date: Jul 2009
Posts: 8
Default most commonly used alignment viewers

Hi there,

I am trying to get a feel for the mosy commonly used/ well regarded alignment viewers out there. I have had a read of the sticky thread outlining what options are available, but Im interested in what people think are well regarded in terms of:

ease of use and well supported
which require local install/ only webtool available
can you navigate in at the genome level (ie. with Affymetrix IGB viewer)
which are more suitable for short/long read data - or one that caters for both
Do they take standard output from commonly used ailgners (velvet/bowtie/maq) - or is there much file manipulation before the viewer can be used.

Are people using SAMtools much?


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Old 08-12-2009, 01:02 AM   #2
NGS specialist
Location: Malaysia

Join Date: Apr 2008
Posts: 249

I have been using the Integrated Genomics Viewer for my short read work.


Heng Li also did a good review of viewers at

IGV works nicely with BED, BAM and GFF files. It does the job for most of my tasks.
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