Lee Katz

I am the senior bioinformatician in the Enteric Diseases Laboratory Branch 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.

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Recent posts

Mash perl module

1 minute read

Hey y’all, I made a new perl module to read and write Mash files.  I made it a complete package, adding it to CPAN with documentation and adding unit testing...

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.”  ...