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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Hash collision experiment

11 minute read

I have talked a bit about hashes with MLST but one crucial issue with hashes is whether they have collisions. In other words, if we have two sequences, there...

What does it take to switch over to BAM from FASTQ? Permalink

less than 1 minute read

I wrote a post on the microbifie blog.

Hash MLST analysis

3 minute read

With EToKi and perhaps future MLST callers, we are possibly looking at a new class of MLST databases 1. I’m not sure which caller was actuall...

List of bioinformatics conferences

16 minute read

Every fiscal year, we have to predict where we are going to travel over the whole next year. However, conferences mainly post on their own website, making no...

Converting a set of VCFs to distances

5 minute read

I think that converting a bunch of VCF files to an alignment is still an artisinal thing. I made this sort of task in the Lyve-SET pipeline back in 2013 and ...