MetaFlow|mics: Nextflow pipelines for metagenomics¶
Cite (Work in progress)¶
MetaFlow|mics: Scalable and reproducible nextflow pipelines for the analysis of microbiome marker data
This repository is a collection of tools for 16S and ITS data analysis and was developed to support scientifics at the Pacific Biosciences Research Center to analyze microbial data. This work was funded by the Hawaii Data Science Institute.
Each analysis tool has been implemented using Nextflow to facilitate their use on any environment, and more specifically on a High Performance Computing Cluster or a Cloud service (GCP, AWS, …). Some configurations are already available in the conf folder (local, hpcc, google cloud). These configurations can be expanded for any other platform.
You will find three available app:
- A demultiplexing app for single or paired barcodes.
- A 16S pipeline for bacterial reads
- An ITS pipeline for fungal reads
See the documentation for more details.
- MetaFlow|mics: Nextflow pipelines for metagenomics
- Getting Started
- Read demultiplexing
- Microbial 16S pipeline
- Fungal ITS pipeline
- Computing resources
- Monitoring your runs with Nextflow Tower
- Linking with the AgaveToGo user interface