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.

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MLST with colorid

2 minute read

I am pleasantly surprised by how well ColorID works with MLST. For some background, please see my previous post on cgMLST.

We can make this beautiful and searchable

1 minute read

You might have seen this message on GitHub for a tab separated file.

Benchmark datasets

1 minute read

Over the last several years, we have been generating benchmark datasets.

The memories

less than 1 minute read

I was cleaning out my office and found a flag that was given to me a few years ago. The legendary Peter Gerner-Smidt had become a citizen and had given some ...

How to call whole genome MLST on the command line

13 minute read

I have been asked in many different contexts how to call alleles on the command line. In August 2022, I gave an internal workshop on how to call alleles on t...