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

Question

[lakhujanivijay]

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?

[cbio]

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.

Answer 1

[mbio.kyle]

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

[John]

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.

Answer 2

[h.mon]

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.

[5heikki]

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 :)

Answer 3

[Vinay Singh]

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

[venu]

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

[lakhujanivijay]

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