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

ADD COMMENTlink 4.0 years ago Vijay Lakhujani 4.1k • updated 4.0 years ago h.mon 25k
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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 4.0 years ago
cbio
• 410
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I use http://www.ruffus.org.uk/ to develop python pipelines for NGS data and it is a great library.

ADD COMMENTlink 4.0 years ago mbio.kyle • 330
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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 4.0 years ago
John
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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 4.0 years ago h.mon 25k
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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 4.0 years ago
5heikki
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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 4.0 years ago Vinay Singh • 40
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This one is also very useful. Other useful links are also provided within that page.

ADD REPLYlink 4.0 years ago
venu
6.2k

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