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.

Main

Recent posts

Cluster detection using Mash

2 minute read

I have been racking my brain on what the command line version of a rapid cluster detection should be.  As in, how can I rapidly figure out if two random geno...

Fixing the R package manager

less than 1 minute read

R’s package manager is broken.  I present to you my solution for it. $HOME is your home directory. 1) mkdir -pv $HOME/R/tmp 2) Edit $HOME/.Renviron and ad...

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...