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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

covid-19-signal

Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.

datasets

Benchmark datasets for WGS analysis

datasets-sars-cov-2

docker-builds

Dockerfiles and documentation on tools for public health bioinformatics

dryad

Dryad is a pipeline to construct reference free core-genome or SNP phylogenetic trees for examining prokaryote relatedness in outbreaks.

gas_scripts_reference

Scripts and reference files to type Group A Streptococcus

gdip

VA DCLS GDIP

gen-epi-at-home

A small genomic epi investigation

oneliners

Useful bash one-liners for bioinformatics.

pangolin

Software package for assigning SARS-CoV-2 genome sequences to global lineages.

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

sars-cov-2_sequencing

A collection of sequencing protocols and bioinformatic resources for SARS-CoV-2 sequencing.

seiscomp

The build environment for all SeisComP repositories. Includes the documentation.

seq_id

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.

staphb_toolkit

Tool kit for public health bioinformatics analysis

tredegar

viral-pipelines

viral-ngs: complete pipelines

wastewatervariantcalling

wgs_competency

Templates for quantitative and graphical reports summarizing bacterial whole genome DNA sequencing competency assessment analyses.