Pinned Repositories
artic-ncov2019
ARTIC nanopore protocol for nCoV2019 novel coronavirus
cdc_read_quality
Generates read-quality metrics using run_assembly_readMetrics.pl from the CDC CG-Pipeline for reads in a specified BaseSpace project.
CDPHE
Various pipelines and scripts used by the CO state public health lab
Cecret
Nextflow workflow for our analysis of SARS-COV-2
centroid
tool to determine optimal refrerence genome given a set of fasta files
Tredegar
docker-builds
:package: :whale: Dockerfiles and documentation on tools for public health bioinformatics
staphb_toolkit
Python Toolkit for using containerized programs in either Singularity or Docker
public_health_bacterial_genomics
public_health_viral_genomics
Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, especially SARS-CoV-2
kevinlibuit's Repositories
kevinlibuit/Tredegar
kevinlibuit/artic-ncov2019
ARTIC nanopore protocol for nCoV2019 novel coronavirus
kevinlibuit/cdc_read_quality
Generates read-quality metrics using run_assembly_readMetrics.pl from the CDC CG-Pipeline for reads in a specified BaseSpace project.
kevinlibuit/CDPHE
Various pipelines and scripts used by the CO state public health lab
kevinlibuit/Cecret
Nextflow workflow for our analysis of SARS-COV-2
kevinlibuit/centroid
tool to determine optimal refrerence genome given a set of fasta files
kevinlibuit/covid-19-signal
Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.
kevinlibuit/datasets
Benchmark datasets for WGS analysis
kevinlibuit/datasets-sars-cov-2
kevinlibuit/docker-builds
Dockerfiles and documentation on tools for public health bioinformatics
kevinlibuit/dryad
Dryad is a pipeline to construct reference free core-genome or SNP phylogenetic trees for examining prokaryote relatedness in outbreaks.
kevinlibuit/GAS_Scripts_Reference
Scripts and reference files to type Group A Streptococcus
kevinlibuit/gdip
VA DCLS GDIP
kevinlibuit/gen-epi-at-home
A small genomic epi investigation
kevinlibuit/oneliners
Useful bash one-liners for bioinformatics.
kevinlibuit/pangolin
Software package for assigning SARS-CoV-2 genome sequences to global lineages.
kevinlibuit/pima-docker
Seperating the Docker Installation and codebase from the core pima codebase. This way the latest version is always created with the latest docker
kevinlibuit/SARS-CoV-2_Sequencing
A collection of sequencing protocols and bioinformatic resources for SARS-CoV-2 sequencing.
kevinlibuit/seiscomp
The build environment for all SeisComP repositories. Includes the documentation.
kevinlibuit/seq_ID
kevinlibuit/snp-pipeline
SNP Pipeline is a pipeline for the production of SNP matrices from sequence data used in the phylogenetic analysis of pathogenic organisms sequenced from samples of interest to food safety.
kevinlibuit/staphb_toolkit
Tool kit for public health bioinformatics analysis
kevinlibuit/viral-pipelines
viral-ngs: complete pipelines
kevinlibuit/WasteWaterVariantCalling
kevinlibuit/wgs_competency
Templates for quantitative and graphical reports summarizing bacterial whole genome DNA sequencing competency assessment analyses.