Curtis Kapsak's repositories
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.
nanoporeWorkflow
:dna: Shell scripts for working with bacterial isolate Nanopore sequence data on CDC servers
docker-builds
:package: :whale: Dockerfiles and documentation on tools for public health bioinformatics
INNUENDO_docker
Docker-compose for INNUENDO Platform deployment
singularities
Singularity recipes for bioinformatics software
centroid
tool to determine optimal refrerence genome given a set of fasta files
datasharing
The Leek group guide to data sharing
INNUENDO_PROCESS_CONTROLLER
INNUENDO Process controller source code wiht integration with Nextflow
INNUENDO_REST_API
Frontend application and REST API for the INNUENDO Platform
INNUENDO_schemas
repository for the INNUENDO chewbbaca schemas
Kalamari
:octopus: A curated database of completed assemblies with taxonomy IDs
Nanopore-data-QC
R code for generating Q-score and read length histograms
nanopore_NCM18
Helpful scripts for working with Oxford Nanopore Sequencing data
prodigal_training_files
species specific training files based on specific reference genomes
ShigaPass
An in silico tool to predict Shigella serotypes
shigatyper
CFSAN Shigella Typing Pipeline
ShigEiFinder
Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies
stxtyper
STX operon typing
stxtyper-ncbi-repo
StxTyper uses a standardized algorithm to accurately type both known and unknown Shiga toxin operons from assembled genomic sequence.
terra-tools
scripts for use with Terra