dmlond / arangs2015 Goto Github PK

• directory structure as per "a quick guide to organizing comp. biol. projects"
• vagrant files and puppet scripts for setting up environments
• shell scripts for running analyses
• small data sets
• (maybe: the html for the course announcement).

Hello, it's been a while!

I was at last year's edition of ARANGS, and I am now starting to use Docker in my job, after using virtual machines for a while. I'd done a makefile to install all the tools that my pipeline requires. Now I'm switching to Docker, I'd like to replace the makefile by my own images.

So I looked at the files from last year, and now I'm wondering if there's a reason for you to use both a bash file and a docker file to install the tools, instead of just using a docker file ? (like this for example : https://github.com/kathrinklee/docker)

Good luck for the next edition of ARANGS, which I believe is coming soon! I liked it a lot last year!

Bye

Claire

...what is it?

In an ideal world we would have a couple of small ones just to show the commonalities even if you are trying to accomplish different scientific goals. Examples that I think might apply to a large number of students:

1. basic quality control: needed by everyone. Includes de-multiplexing (e.g. by adaptors/barcodes and/or by primers), trimming low quality reads, visualizing quality distributions

2a. mapping to a reference, using bwa. Requires a small reference, e.g. a chloroplast / mitochondrion / small chromosome / bacterium and a small-ish set of reads. Index the reference, map against it (paired end?), create a BAM file, visualize it.

2b. de novo assembly, using soapdenovo (?). Requires a small-ish set of reads. Optimize kmer size (kmergenie?), run the assembly, calculate statistics (N50).

2c. diversity assessment, using QIIME (?). Requires a small-ish set of reads - not too short, maybe IonTorrent or 454 (?). Cluster the reads, blast exemplars, build tree, compare samples (unifraq).

GitHub: I guess that the expectation was that we would state that we would teach them to use repositories and versioning from scratch. Which we will, for sure.
Can we say it more explicitly? Maybe in the timetable?