A simple pipeline for bacterial assembly and quality control

CDCgov/mycosnp-nf

🔄 Github action to sync your forks

Cut And Run Analysis Pipeline

An easy-to-use, flexible variant calling pipeline for use on the Biowulf cluster at NIH

Dryad is a Nextflow pipeline for examining prokaryote relatedness. Dryad can perform a reference free analysis and/or SNP analysis.

🔥🐦🔥PHoeNIx: a platform agnostic pipeline for healthcare-associated and antimicrobial resistant pathogens

AR Report Generator is used to render a report from the output of pipelines that identify antibiotic resistance (AR) genes and/or examine prokaryote relatedness in outbreaks

Mouse nEoanTigen pRedictOr

CCBR related projects

Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.

Reference-based consensus creation

A collection of Dockerfiles to facilitate reproducibility across computing environments.

RNA Biology Pipeline to Characterize protein-RNA Interactions

CGR's QIIME microbiome pipeline

Antimicrobial Resistance Characterization in Metagenomes