<p>Hi all, </p>

<p>I guess most people here are using open source/command line tools for NGS analysis.  Nonetheless I am wondering if anyone has experience with any of the major commercial analysis suites and what your opinions are on them.</p>

<p>Undoubtedly there is a loss of flexibility and transparency when we move to an analysis suite but they have their obvious advantages also.  </p>

<p>I am not so much concerned with proprietary algorithms etc so much as I am thinking of usability, stability, flexibility, etc... </p>

<p>I have been very impressed by the <a href="http://www.clcbio.com/index.php?id=1240">CLC Genomics Workbench</a> and I have been recommending it to most of the life scientists regardless of their computational background. </p>
<p>It is particularly handy to study small genomes (10-100Megabases) that can be processed easily on a more powerful desktop. For many tasks I find it amazingly potent way to save time - rule out certain hypothesis, explore potential alternatives. </p>
<p>For example right now I have a dataset of 9 million 70bp reads on a bacteria of 4 Megabases. I can assemble that with three four clicks, or align to one reference or another, or blast the largest contigs - each task takes just a a few clicks and probably  about five minutes of my time to set all that up - then I can do something else while it runs. If something good comes up I can move onto a more thorough process. Most impressively it does both the assembly and mapping faster and using less resources than most alternatives.</p>
<p>To use it I don't need to remember how to run Velvet or some other assembler, how to index the genome for mapping, pick the right parameters, etc. Compared to the overall cost of sequencing or that of my time the a license for CLC is very cheap. </p>
<p>If everyone could just use a tool like CLC and only asked for questions that cannot be solved by it - most people's research would be a lot farther ahead  it would allow people to spend more of their brain power on complex tasks rather than simple things.</p>