Question: NGS pipeline - clusterflow
0
gravatar for ganeshhyd97
5.7 years ago by
India
ganeshhyd970 wrote:

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

ngs pipelines • 2.0k views
ADD COMMENTlink modified 5.7 years ago • written 5.7 years ago by ganeshhyd970
1

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.  

ADD REPLYlink written 5.7 years ago by HG1.1k
1
gravatar for RamRS
5.7 years ago by
RamRS30k
Baylor College of Medicine, Houston, TX
RamRS30k wrote:

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.

ADD COMMENTlink written 5.7 years ago by RamRS30k

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.

ADD REPLYlink modified 5.7 years ago by RamRS30k • written 5.7 years ago by ganeshhyd970
0
gravatar for mikhail.shugay
5.7 years ago by
mikhail.shugay3.4k
Czech Republic, Brno, CEITEC
mikhail.shugay3.4k wrote:

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.

ADD COMMENTlink modified 5.7 years ago • written 5.7 years ago by mikhail.shugay3.4k
0
gravatar for ganeshhyd97
5.7 years ago by
India
ganeshhyd970 wrote:

thank you. I will check it out.

ADD COMMENTlink written 5.7 years ago by ganeshhyd970

Hi ganeshhyd97,

This reply is better suited as a comment on mikhail's answer. Could you make the appropriate change please? That would involve the following steps:

Copy the contents of your reply from this answer
Click on "Add Comment" on mikhail's post here: A: NGS pipeline - clusterflow
Paste the copied text
Click on the green "Add Comment" button

Thank you!

ADD REPLYlink written 5.7 years ago by RamRS30k
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