There are roughly a zillion ways to visualize SAM/BAM data, from homebrewed perl scripts to GUI-button laden programs like IGV, and to this zillion I'm adding yet another: Samscope. Samscope was born out of dissatisfaction with the awkwardness of other visualization software, and the desire for something that can pan and zoom as fast and naturally as we've become accustomed to with things like Google maps, and hopefully help to answer (and inspire) questions from curious biologists who see something unusual and go "what's causing that??". The key features that separate it from other visualization software are:
To be fair, IGV can do a lot of these if you work at it, but I think Samscope makes a lot of these much easier, does some of them much much better, and in general runs much faster.
I'm sure I've introduced some new awkwardness, but so far it's been quite useful for the project I've used it on, and has been accepted by Bioinformatics, and has been downloaded a lot, so somebody's using it (or at least trying to)! If anyone here in the seqanswers community has questions, or feature requests, please feel free to use this thread.
There's binary (and source) packages published for Ubuntu and Debian, and it's known to work on CentOS and Fedora (sorry, no .rpms yet). If you're daring, I'll bet it would work in Mac OS X and Cygwin if you can satisfy the library dependencies, but this is untested territory (patches/pull requests to make this easier are of course welcome!).
If this isn't at all helpful or interesting to you, please forgive this post blatantly hawking my own GPL wares
- automatic generation of aggregate feature layers (like coverage, polarity (aka strand bias. very helpful for ChIP-Seq!), mutations, indels, minor allele frequency, etc).
- visualization of a full distribution of values even while zoomed way out (see the 'c' key).
- ability to view these layers simultaneously overlaid in different colors or in multiple synchronized windows.
- include data from separate data files as separate but simultaneously viewable layers (again: different colors or multiple windows).
- intuitive read inspection, closely integrated with main viewer.
- paired end classification and visualization.
- simple consensus calling, handy for mutation search.
- batch operation for automated image generation.
- tuning-free operation on any SAM/BAM file with headers (no need for pre-defining chromosome names/sizes/etc., or even a reference FASTA file!).
- support for annotation formats like GTF/GFF, WIG/BED, etc.
To be fair, IGV can do a lot of these if you work at it, but I think Samscope makes a lot of these much easier, does some of them much much better, and in general runs much faster.
I'm sure I've introduced some new awkwardness, but so far it's been quite useful for the project I've used it on, and has been accepted by Bioinformatics, and has been downloaded a lot, so somebody's using it (or at least trying to)! If anyone here in the seqanswers community has questions, or feature requests, please feel free to use this thread.
There's binary (and source) packages published for Ubuntu and Debian, and it's known to work on CentOS and Fedora (sorry, no .rpms yet). If you're daring, I'll bet it would work in Mac OS X and Cygwin if you can satisfy the library dependencies, but this is untested territory (patches/pull requests to make this easier are of course welcome!).
If this isn't at all helpful or interesting to you, please forgive this post blatantly hawking my own GPL wares
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