Re: [DIYbio] How much bioinformatics at your DIY lab?

I'm interested in coming up with beginner to intermediate-level  bioinformatics projects for my local DIY bio group. I think I'm okay  with figuring out what tools to use, but I'm a bit fuzzy on where to  find data to play with. With regards to the "Illumina short reads,  PacBio long reads, and optical mapping data", did you obtain all of this  data yourself first-hand from your own samples? If not, where might one  look to find freely available data to experiment with?    -Brendan

In addition to what Dan said, at TheLab most of the bioinformatics if you want to call it that is just folks using Snapgene to plan out molecular cloning activities.  On a few occasions I have tried to get group bioinformatics projects going but they tend to fizzle out quickly.

There's a lot of low-hanging fruit and I think community labs have the ability to tackle some grand problems. But I have found organization and communication to be the largest hindrance to progress. A small group of people who speak the same technical lingo can make quick progress but once you have a large group with varying education backgrounds, we spend so much time laying out the basics that the more advanced folks get bored and disperse and the project quietly dies.

The most advanced thing we've done is assemble a bacteria genome combining Illumina short reads, PacBio long reads and optical mapping data to put together a mostly complete draft chromosome.

-Cory