although this question may sound very similar to a previous one posted months ago, I was wondering if there would be any news on that. we are currently setting up our brand new cluster by installing the required software for data analysis, and although we already know what we are going to install, it's never useless to know how other groups are solving this task. for that reason, I am sharing here our production ideas, as well as some testing ones that we would like to try, for you to give us our opinion or either suggest other tools.
we have been installing BioScope for a long time. it was our first software choice, since it is the corporative one, plus it is free of charge (right now). the problem is that, as we did not buy the suggested cluster, although we followed up all the software requirements, setting up our "custom" cluster has been taking Life Technologies almost 2 months, and we still do not have it up and running. we will see if we are able to have it ready by next month ;)
our second option has been reading all the papers around we could, as well as asking some other laboratories, trying to find a consensus in which software to use, at least for mapping and SNP calling. after quite a few weeks of discussion, we have finally decided to create a custom pipeline based on BFAST (we have been told that it was the one that is currently best performing with SOLiD data) and SAMtools' Pileup. we are currently testing this pipeline, and we are being quite happy with it, although getting it to work exactly as we would like to needs further progress.
although I have not done anything deep with Galaxy, I have found it very useful in the past for basic data manipulation. recentrly, I have gratefully found out that it has integrated NGS functionalities that would allow us to deal with our SOLiD data by mapping it with Bowtie (I have read that it is a nice BWT implementation, and that it works fine with SOLiD data) and doing SNP calling with SAMtools. since working with large datasets forces us to install Galaxy locally we are carefully evaluating this possibility, because it looks useful enough to try it, specially thinking about having everything nicely integrated in a single user interface.
EDIT: it turns out that we are currently installing Galaxy locally on our cluster, and we have found that the NGS toolbox beta from the usegalaxy.org website is no longer in beta stage, and indeed the mapping section includes more options, such as BFAST (indeed, the aligner we wanted to build our pipeline with).
are there any groups out there working with BioScope only? are you happy enough not to try other options? is it as stable and powerful as advertised?
which programs are you using for SOLiD data analysis? why would you select them?
does anyone currently rely on Galaxy only for processing SOLiD data? is the local installation clear and stable enough to go through it? would you recommend