Question: What are some good resources to learn shell script for NGS pipeline development?
5
gravatar for lakhujanivijay
4.0 years ago by
lakhujanivijay4.7k
India
lakhujanivijay4.7k wrote:

What are some good resources to learn shell script for NGS pipeline development?

How much shell script should one know to develop an intermediate level pipeline for NGS data analysis?

Can someone suggest some good resources, tutorials?

pipeline ngs shell script • 2.9k views
ADD COMMENTlink modified 4.0 years ago by h.mon29k • written 4.0 years ago by lakhujanivijay4.7k
3

I suggest looking into Snakemake. It's an excellent tool for developing NGS pipelines with good documentation, and is easy to use.

That being said, it may require some very basic background in the Unix command line, and bash. Python for the more advanced options as well.

ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by cbio430
4
gravatar for mbio.kyle
4.0 years ago by
mbio.kyle360
United States
mbio.kyle360 wrote:

I use http://www.ruffus.org.uk/ to develop python pipelines for NGS data and it is a great library.

ADD COMMENTlink written 4.0 years ago by mbio.kyle360

I have never heard of this before, but I have to say if you know python this is great. I like how it's all done with just a few simple decorators.

ADD REPLYlink written 4.0 years ago by John12k
4
gravatar for h.mon
4.0 years ago by
h.mon29k
Brazil
h.mon29k wrote:

What is an "intermediate level pipeline"? What is your target audience? Release the pipeline into the wild? Internal lab use? Personal use? Anyway, to learn shell scripting for NGS pipeline development, you must learn shell scripting, so look at the "Bash Guide for Beginners" and "Advanced Bash-Scripting Guide".

With a very basic understanding of bash scripting you may easily put together a simple pipeline which will, for example, clean your reads, assemble a genome, map the reads / additional reads into assembled genome, and annotate assembled genome. In fact, I wrote such simple pipeline - it is really crude, no error checking, no optimizations, no whatever, but I feed fastq files and some hours later get a draft genome and its annotation.

ADD COMMENTlink written 4.0 years ago by h.mon29k

These are IMO the best links in this thread. This material covers essentially everything related to Bash scripting. I still visit this site from time to time myself :)

ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by 5heikki8.6k
2
gravatar for Vinay Singh
4.0 years ago by
Vinay Singh40
INDIA, New Delhi, JNU
Vinay Singh40 wrote:

Here are some good links that you can try. 1.http://lh3lh3.users.sourceforge.net/biounix.shtml 2.http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/linux.html

ADD COMMENTlink written 4.0 years ago by Vinay Singh40

This one is also very useful. Other useful links are also provided within that page.

ADD REPLYlink written 4.0 years ago by venu6.3k

@venu would you mind editing the link above which appears to be broken?

ADD REPLYlink written 4 months ago by lakhujanivijay4.7k
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