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followers: 178.0 following: 82.0 repos: 157.0 gists: 13.0

Name: Lee Katz

Type: User

Company: CDC (work) + personal projects

Twitter: lskatz

Location: Atlanta, GA

Blog: https://lskatz.github.io

Hi there 👋

I am a bioinformatician in the Enteric Diseases Laboratory Branch at CDC. My repos include those for work and those for outside of work.

I speak 🐫 perl, ⚙️ rust, and 🐬 SQL
I pretend to speak 🙄 R and 🐍 Python.
😵 In my past lives, I used to code PHP, HTML, CSS, JavaScript, and even some C.

I have worked on some perl modules including Bio::Kmer but also more complete packages such as Mashtree and Lyve-SET. I have more in my repos and would be glad to collaborate with you!

For more information

Google Scholar profile page https://scholar.google.com/citations?user=7ye89WMAAAAJ&hl=en
My about page https://about.me/lskatz

Lee Katz's Projects

advent-of-code

https://adventofcode.com/

allelecodes

Python script(s) for assigning allele codes under current PulseNet nomenclature system in BioNumerics but as a command-line executable without BioNumerics dependencies

amplicon_coverage_plot

interactive barplot for amplicon sequencing

ani-m

Average Nucleotide Identity analysis with MUMmer under the hood

anitree

Create trees using ANI

annapotater

Quick and dirty SNP annotator

any2bed

Convert files to bed format

any2index

app-perlbrew

Manage perl installations in your $HOME

awesome-advent-of-code

A collection of awesome resources related to the yearly Advent of Code challenge.

awesome-bioinformatics-education

resources for bioinformatics education

awesome-bioinformatics-jobs

Resources for bioinformatics jobs

awesome-github-templates

:octocat: Curated list of GitHub Issues and Pull Requests templates

bactopia

A flexible pipeline for complete analysis of bacterial genomes

bactopia-workshop

A workshop on getting started with Bactopia

bigsi_rs

Rust in-memory implementation of a BIGSI-like data structure

bio

Bioinformatics library for .NET

bio--kmer

A perl module for kmer counting

bio--minimizer

Bioinformatics perl module for minimizers

bio-js

Lee Katz's original bio-javascript library

bio-phylo

Bio::Phylo - Phyloinformatic analysis using Perl

bio-sketch-perl

Pure perl implementation of min-hash sketching. Might not be compatible with Mash.

bioconda-recipes

Conda recipes for the bioconda channel.

bioperl-live

Core BioPerl 1.x code

biophp

Lee Katz's BioPHP

biophp-at-ga-tech

Bioinformatics tools for PHP

bookai

Machine learning for making my novel

c-wap

SC2 variant detection and composition pipeline

callsam

Call variants on sam files

cdcgov.github.io

Portal site for all CDCgov projects, https://cdcgov.github.io

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