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Hi there šŸ‘‹

Hi! I'm Curtis. I'm a bioinformatician working with Theiagen Genomics. I'm a fan of microbial genomics šŸ¦ , reproducible bioinformatics methods ā™»ļø, and DNA sequencing šŸ§¬!

  • šŸŒ± Iā€™m currently learning Python, WDL, Nextflow, and Continuous Integration techniques
  • šŸ‘Æ Iā€™m looking to collaborate on developing dockerfiles to make installation and usage of bioinformatics tools easier! See here
  • šŸ’¬ Ask me about - Microbial & viral genomes, plasmids, software containers
  • šŸ“« How to reach me - Twitter, LinkedIn, email kapsakcj (at) gmail (dot) com,
  • šŸ˜„ Pronouns - He/Him

Curtis Kapsak's Projects

centroid icon centroid

tool to determine optimal refrerence genome given a set of fasta files

docker-builds icon docker-builds

:package: :whale: Dockerfiles and documentation on tools for public health bioinformatics

kalamari icon kalamari

:octopus: A curated database of completed assemblies with taxonomy IDs

nanopore_ncm18 icon nanopore_ncm18

Helpful scripts for working with Oxford Nanopore Sequencing data

nanoporeworkflow icon nanoporeworkflow

:dna: Shell scripts for working with bacterial isolate Nanopore sequence data on CDC servers

scripts icon scripts

Various pipelines and scripts used by the CO state public health lab

shigapass icon shigapass

An in silico tool to predict Shigella serotypes

shigeifinder icon shigeifinder

Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies

snp-dists icon snp-dists

Pairwise SNP distance matrix from a FASTA sequence alignment

win10-linux-conda-how-to icon win10-linux-conda-how-to

A tutorial on how to set up a Linux environment on a computer running Windows 10. Followed by how to install and use (bio)conda.

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