garfinjm

HAI-Seq

HAI_QC: Scripts for performing QC on sequencing data prior to upload to NCBI

aaa24_nf

aaanf

alignment_training

aquascope

artic-ncov2019

ARTIC nanopore protocol for nCoV2019 novel coronavirus

augur-nf

Nextflow implementation of Nextstrain's Augur pipeline

bioconda-recipes

Conda recipes for the bioconda channel.

Cecret

Reference-based consensus creation

central-region

Site for AMD Central Region

docker-builds

:package: :whale: Dockerfiles and documentation on tools for public health bioinformatics

legsta-nf

Nextflow wrapper for read cleaning, assembly, and legionella SBT from short reads

MNextstrain

mnotfieldbioinformatics

The ARTIC field bioinformatics pipeline - a fork that tries to not suck

modules

Repository to host tool-specific module files for the Nextflow DSL2 community!

ncov

Nextstrain build for novel coronavirus SARS-CoV-2

primer-schemes

Primer schemes for real-time genome epidemiology

qmk_firmware

Open-source keyboard firmware for Atmel AVR and Arm USB families

serotypefinder-nf

E. coli serotyping typing from raw reads

staph-b.github.io

Visit the site here:

staphb_toolkit

Python Toolkit for using containerized programs in either Singularity or Docker

teaspoon

Quickly downsample Illumina PE reads to an approximate coverage, without a known genome size.