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coding, coding, coding
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coding, coding, coding
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Arctic Code Vault Contributor

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@ncezid-biome
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lskatz/README.md

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

Pinned

  1. mashtree Public

    🌳 Create a tree using Mash distances

    Perl 70 12

  2. lyve-SET Public

    💃 🌴 LYVE-SET, a method of using hqSNPs to create a phylogeny, especially for outbreak investigations

    Perl 18 16

  3. SneakerNet Public

    🐾 QA/QC pipeline for a MiSeq/HiSeq/Ion Torrent/assembly-only run

    Perl 7 3

  4. fasten Public

    👷 Fasten toolkit, for streaming operations on fastq files

    Rust 22 4

  5. Kalamari Public

    🐙 A curated database of completed assemblies with taxonomy IDs

    Perl 23 2

  6. tongzhouxu/mashpit Public

    📝 Sketch-based surveillance platform

    Python 6 2

447 contributions in the last year

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Contribution activity

September 2021

Created 9 commits in 6 repositories
Created 7 repositories

Created a pull request in nf-core/modules that received 19 comments

added classic mlst module

PR checklist Closes #XXX This comment contains a description of changes (with reason). If you've fixed a bug or added code that should be test…

+187 −0 • 19 comments
Opened 3 other pull requests in 3 repositories
hcdenbakker/sepia 1 closed
hcdenbakker/bigsi_rs 1 merged
lskatz/any2index 1 merged

Created an issue in tseemann/mlst that received 2 comments

cgMLST database creation documentation

I am trying to make a guide for myself to create a cgMLST or even a wgMLST scheme. I hope this helps others. I suggest adding this in some way to t…

2 comments
Opened 7 other issues in 7 repositories
tseemann/prokka 1 open
bactopia/bactopia 1 open
lskatz/fasten 1 open
tseemann/mlst 1 open
lskatz/any2index 1 open
samtools/samtools 1 open
shogo82148/actions-setup-perl 1 open
Started 1 discussion in 1 repository
kjolley/BIGSdb

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