Curtis Kapsak's Projects
tool to determine optimal refrerence genome given a set of fasta files
The Leek group guide to data sharing
:package: :whale: Dockerfiles and documentation on tools for public health bioinformatics
Docker-compose for INNUENDO Platform deployment
INNUENDO Process controller source code wiht integration with Nextflow
Frontend application and REST API for the INNUENDO Platform
repository for the INNUENDO chewbbaca schemas
:octopus: A curated database of completed assemblies with taxonomy IDs
R code for generating Q-score and read length histograms
Helpful scripts for working with Oxford Nanopore Sequencing data
:dna: Shell scripts for working with bacterial isolate Nanopore sequence data on CDC servers
species specific training files based on specific reference genomes
R Recipes
Various pipelines and scripts used by the CO state public health lab
An in silico tool to predict Shigella serotypes
CFSAN Shigella Typing Pipeline
Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies
Singularity recipes for bioinformatics software
Pairwise SNP distance matrix from a FASTA sequence alignment
STX operon typing
scripts for use with Terra
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.