Next Gen. data analysis requires many steps, that can be learned one by one, for example running an aligner such as bowtie, tophat or STAR, then handle the SAM/BAM file for subsequent analysis.
Once the various steps are understood and if there are new analyzes do be performed routinely, it would be “nice” to have access to a method that combines all or most of the steps in a “pipeline” for mostly automated analyzes. Furthermore this system would be even better if it could handle various types of analyzes (RNA-seq, Chip-Seq, SNP etc.).
One solution can be found at pythonhosted.org/omics_pipe that, in addition offers an Amazon Cloud (AWS) solution as well as a local installation option.
The documentation is very detailed for either installation, and also contains a step-by-step tutorial.
Once the system is in place, the pipeline is engaged by a single “parameters file” that contain simple lines to define directories and what to do in a very simple line-by-line form, for example:
Installing such a system may require help from the IT department of the System administrator, and should only be considered if planning more than just one experiment or analysis as this will take to time to set-up. But once set-up the gain of time will be obvious.
Note: Complete page content of the site: http://pythonhosted.org/omics_pipe/contents.html