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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.
- Atlanta, GA
- CDC (Work) + Personal Projects
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. Follow.
- Overview
- Two modes: fast or accurate
- Further documentation
- References
- Citation
Create a tree using Mash distances.
For simple usage, see mashtree --help. This is an example command:
Input files: fastq files are interpreted as raw read files. Fasta, GenBank, and EMBL files are interpreted as genome assemblies. Compressed files are also accepted of any of the above file types. You can compress with gz, bz2, or zip.
Output files: Newick (.dnd). If --outmatrix is supplied, then a distance matrix too.
For perl library help, run perldoc on a .pm file, e.g., perldoc lib/Mashtree/Db.pm.
For executable help run --help, e.g., mashtree_bootstrap.pl --help.
For more information and help please see the docs folder
For more information on plugins, see the plugins folder. (in development)
JOSS
Katz, L. S., Griswold, T., Morrison, S., Caravas, J., Zhang, S., den Bakker, H.C., Deng, X., and Carleton, H. A., (2019). Mashtree: a rapid comparison of whole genome sequence files. Journal of Open Source Software, 4(44), 1762, https://doi.org/10.21105/joss.01762
Poster
Katz, L. S., Griswold, T., & Carleton, H. A. (2017, October 8-11). Generating WGS Trees with Mashtree. Poster presented at the American Society for Microbiology Conference on Rapid Applied Microbial Next-Generation Sequencing and Bioinformatic Pipelines, Washington, DC. Poster number 27.
Kalamari. A database of completed assemblies for metagenomics-related tasks. Synopsis. Kalamari is a database of completed and public assemblies, backed by trusted institutions. These assemblies can be further used in formatted databases such as Kraken or Blast. Prerequisites & Recommendations. Requirements:
Apr 26, 2023 · 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. Follow. Atlanta, GA, USA.
- Lee Katz
Lee Katz is the senior bioinformatician in the Enteric Diseases Laboratory Branch at CDC. He graduated with a PhD in bioinformatics in 2010 from GA Tech and has worked at CDC since then.
Jun 2, 2010 · View Lee Katz’s profile on LinkedIn, a professional community of 1 billion members. Bioinformatician at Centers for Disease Control and Prevention · I am the senior bioinformatician in the ...
- Websites
