Lee Katz

I am a bioinformatician at CDC. In my free time, I try to be a good husband and parent, and in my imaginary free time, I podcast with my co-hosts on the Micro Binfie podcast. All opinions are my own and are not necessarily shared by my employer.

Main

Recent posts

Sampling the taxonomy database

1 minute read

I was a little frustrated that every time I wanted to try out my new Bio::DB::Taxonomy-based script, it would take a few minutes to run…. and then I would fi...

Custom Kraken database

2 minute read

Like many labs around the world, we use Kraken for contamination detection.  This isn’t its intended purpose however because it is supposed to be a taxonomic...

Tree To Reads

less than 1 minute read

It looks like Tree To Reads is online in a preliminary draft!  I encourage everyone to try it out! http://biorxiv.org/content/early/2016/01/22/037655 Using...

Perl writing style

6 minute read

I’m taking a moment to reflect on a post that Torsten Seemann wrote a couple of years ago called “Minimum standards for bioinformatics command line tools.”  ...

Krona snippet

less than 1 minute read

I couldn’t find any kind of conversion Kraken and Krona recently and so I wrote up a little pipeline.  Full script is available at lskScripts: https://github...