AB SOLiD Bioscope

[drio]

Bioscope has, in theory, a very nice workflow where you specify a 'plan' of modules to use for a given project. As an example the 'plan' may call the 'quality value filter' module, then the 'mapping' module, then in parallel the 'mapping statistics' module plus the 'GFF' module. And so on. Each module has their own 'ini' (initialization) file which in addition to per-module commands can read in a global ini file and a per-project ini file. Once you have a 'plan' set up then you just hand it off to the workflow schedule and it runs the project.

All very nice. Except ... the ini files do not pass information between each other. Nor do they use consistent parameter names. Some of the parameters are used but undocumented. The modules make unwarranted assumptions on what the previous module has done. A common example involves file names where the output file name of a module may not be in the format that the next module can understand as its input file name. Ditto with other parameters. I set a parameter in the per-project ini file and expect it to filter down through the modules -- which it does to the most part but I will often find at least one module which does not accept the parameter.

That is what I mean by 'fragile' and 'fall apart'. Touch or change one small part of the plan and the pipeline fails.

Of course this is version 1.0 of Bioscope. The software is really only used by a handful of people (as compared to, say, Microsoft Word). Thus we should expect that we will be de-facto beta testers and will encounter rough spots. Lifetech/ABI support is very responsive in trying to fix problems that I find.

Thanks for sharing,

My five cents:

PROs:

+ dramatic improvement in terms of running time compared with CL
+ increase of sensitivity with same specificity.
+ Much more resource efficient both IO and CPU (it is multithreaded now)
+ Easier to start analysis (at least compared to corona lite)

CONs:

+ Still to many unnecessary files being generated
+ BAM is not the standard format to drop the alignments. Valuable
CPU cycles and I/O bandwidth wasted in postprocessing.
+ Changes in the reporting stats don't match the old corona lite. They mainly
report uniquely mapped reads.

[westerman]

Bioscope has, in theory, a very nice workflow where you specify a 'plan' of modules to use for a given project. As an example the 'plan' may call the 'quality value filter' module, then the 'mapping' module, then in parallel the 'mapping statistics' module plus the 'GFF' module. And so on. Each module has their own 'ini' (initialization) file which in addition to per-module commands can read in a global ini file and a per-project ini file. Once you have a 'plan' set up then you just hand it off to the workflow schedule and it runs the project.

All very nice. Except ... the ini files do not pass information between each other. Nor do they use consistent parameter names. Some of the parameters are used but undocumented. The modules make unwarranted assumptions on what the previous module has done. A common example involves file names where the output file name of a module may not be in the format that the next module can understand as its input file name. Ditto with other parameters. I set a parameter in the per-project ini file and expect it to filter down through the modules -- which it does to the most part but I will often find at least one module which does not accept the parameter.

That is what I mean by 'fragile' and 'fall apart'. Touch or change one small part of the plan and the pipeline fails.

Of course this is version 1.0 of Bioscope. The software is really only used by a handful of people (as compared to, say, Microsoft Word). Thus we should expect that we will be de-facto beta testers and will encounter rough spots. Lifetech/ABI support is very responsive in trying to fix problems that I find.

[drio]

Can you be more specific? What do you mean fall apart?

[westerman]

Bioscope seems ... fragile ... at the moment. Fragile in the sense that I can run all of the test examples just fine and they seemly give good results. But when I modify the scripts to work with my data then things fall apart.

[drio]

I have been using it for re-sequencing (still testing). BS bundles a bunch of different experiment, WT among them. I would say, download the software and start by
running the examples that come with it. Once you have it up and running modify it
to work with your data and test it out.
ABi supports SGE and PBS. THe installation in non-root mode is not extremely invasive so I would suggest you start by that.

Let us know how it goes.

[rdeborja]

Is anyone using/testing Bioscope as a replacement for corona lite and the whole transcriptome pipeline? I've recently installed it on our cluster and was curious to find other opinions/experiences with it.