NGS pipeline - clusterflow

Question

[ganeshhyd97]

Dear all

I am an Computer science person and please excuse me for this silly question. Just installed and configured a SGE cluster which will be used for NGS applications in my organisation. I am interested to understand the NGS techniques and like to develop pipelines. Installed cluster flow pipeline and tried executing the existing pipelines with some sample data and reference genomes. It seems to work well. Please help me to know the sequence in NGS techniques so that it will be helpful for me to develop pipelines.

or clusterflow is sufficient for all NGS techniques.

Thanks

Ganesh

[HG]

Hello Ganesh, Could you please let us to know what do you need exactly I mean then it will be better to provide some information.

Answer 1

[Ram]

From what I see here, CF is a wrapper to work with custom pipelines, that in turn will work with the actual underlying software. So, CF will not be sufficient, you'll need the actual underlying software, then maybe write pipelines that users can run.

[ganeshhyd97]

Thanks for your reply. But to write pipeline I should now all the processes (and best tools of each process) involved in NGS techniques. Is there any fixed steps for example in whole genome seq. Googling gives different answers and is confusing. Please clarify.

Answer 2

[mikhail.shugay]

So you want some example pipelines to see how it works in practice? I can suggest checking out the Blue Collar Bioinformatics project. You can find lots of comprehensive benchmarks here: http://bcb.io/. You can also check out the code at https://github.com/chapmanb/bcbio-nextgen: it is quite straightforward to derive steps for most pipelines using it.

[ganeshhyd97]

thank you. I will check it out.