MetaFlow|mics: Nextflow pipelines for metagenomics

Cite

Cédric Arisdakessian, Sean B. Cleveland, and Mahdi Belcaid. 2020. MetaFlow|mics: Scalable and Reproducible Nextflow Pipelines forthe Analysis of Microbiome Marker Data. InPractice and Experience in Advanced Research Computing (PEARC ’20), July 26–30, 2020,Portland, OR, USA.ACM, New York, NY, USA, 9 pages.

Description

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:

1. A demultiplexing app for single or paired barcodes.
2. A 16S pipeline for bacterial reads
3. An ITS pipeline for fungal reads

See the documentation for more details.

Contribute

• Issue tracker: GitHub
• Source Code: GitHub

License

Apache 2.0

Contents:

• MetaFlow|mics: Nextflow pipelines for metagenomics
• Getting Started
  • Downloading the pipelines
  • Usage
  • Choosing the pipeline parameters
  • Dependencies
  • Configuration profiles
• Read demultiplexing
  • Pre-requisites
  • Usage
  • Demultiplexing steps
• Microbial 16S pipeline
  • Pre-requisites
  • Usage
  • Outputs
  • 16S pipeline steps
• Fungal ITS pipeline
  • Pre-requisites
  • Usage
  • ITS pipeline steps
• Computing resources
  • Main parameters
  • Configure for a HPCC
  • Configure for Google Cloud Plateform (GCP)
  • Configure for Amazon Web Service
• Monitoring your runs with Nextflow Tower
• Linking with the AgaveToGo user interface

Indices and tables

• Index
• Module Index
• Search Page