kapsakcj
Bioinformatics Scientist. Member of StaPH-B (State Public Health Bioinformaticians)
@theiagenRichmond, VA
Pinned Repositories
docker-builds
:package: :whale: Dockerfiles and documentation on tools for public health bioinformatics
INNUENDO_docker
Docker-compose for INNUENDO Platform deployment
kapsakcj
nanoporeWorkflow
:dna: Shell scripts for working with bacterial isolate Nanopore sequence data on CDC servers
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.
docker-builds
:package: :whale: Dockerfiles and documentation on tools for public health bioinformatics
public_health_bacterial_genomics
public_health_bioinformatics
Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health concern.
public_health_viral_genomics
Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, especially SARS-CoV-2
kapsakcj's Repositories
kapsakcj/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.
kapsakcj/nanoporeWorkflow
:dna: Shell scripts for working with bacterial isolate Nanopore sequence data on CDC servers
kapsakcj/docker-builds
:package: :whale: Dockerfiles and documentation on tools for public health bioinformatics
kapsakcj/INNUENDO_docker
Docker-compose for INNUENDO Platform deployment
kapsakcj/kapsakcj
kapsakcj/r-recipes
R Recipes
kapsakcj/singularities
Singularity recipes for bioinformatics software
kapsakcj/snp-dists
Pairwise SNP distance matrix from a FASTA sequence alignment
kapsakcj/centroid
tool to determine optimal refrerence genome given a set of fasta files
kapsakcj/curtis-utilities-and-configs
random scripts for various purposes
kapsakcj/datasets-sars-cov-2
kapsakcj/datasharing
The Leek group guide to data sharing
kapsakcj/INNUENDO_PROCESS_CONTROLLER
INNUENDO Process controller source code wiht integration with Nextflow
kapsakcj/INNUENDO_REST_API
Frontend application and REST API for the INNUENDO Platform
kapsakcj/INNUENDO_schemas
repository for the INNUENDO chewbbaca schemas
kapsakcj/Kalamari
:octopus: A curated database of completed assemblies with taxonomy IDs
kapsakcj/Nanopore-data-QC
R code for generating Q-score and read length histograms
kapsakcj/nanopore_NCM18
Helpful scripts for working with Oxford Nanopore Sequencing data
kapsakcj/prodigal_training_files
species specific training files based on specific reference genomes
kapsakcj/SARS-CoV-2_Sequencing
kapsakcj/scripts
Various pipelines and scripts used by the CO state public health lab
kapsakcj/ShigaPass
An in silico tool to predict Shigella serotypes
kapsakcj/shigatyper
CFSAN Shigella Typing Pipeline
kapsakcj/ShigEiFinder
Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies
kapsakcj/SneakerNet
kapsakcj/stxtyper
STX operon typing
kapsakcj/stxtyper-ncbi-repo
StxTyper uses a standardized algorithm to accurately type both known and unknown Shiga toxin operons from assembled genomic sequence.
kapsakcj/terra-tools
scripts for use with Terra
kapsakcj/wdl_scripts