UPHL's Reference Free Pipeline

Reference-based consensus creation

A Nextflow pipeline for viral genomics (Influenza/RSV) supporting Illumina and Nanopore sequencing of clinical and wastewater samples.

The scripts that UPHL uses to download things from basespace and run respective workflows

Assembly of Nanopore Sequencing

A collection of Dockerfiles for the images that we use

Nextflow pipeline for Neisseria gonorrhoeae isolate analysis

CDCgov/mycosnp-nf

To be able to run Nextflow scripts that are published on Github on ICA they must be modified because ICA does not have Nextflow do a gitpull and an ICA user cannot pass config or param files.