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Introduction

nfcore/nanodemux is a bioinformatics analysis pipeline that can be used to demultiplex, QC and map Nanopore data.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.

Pipeline Summary

  1. Basecalling, barcoding and adapter trimming (Guppy; optional)
  2. FastQ QC (NanoPlot)
  3. Alignment (GraphMap or minimap2)
    • Convert .sam to co-ordinate sorted .bam and obtain mapping metrics (SAMtools)
  4. Present QC for alignment results (MultiQC)

Documentation

The nf-core/nanodemux pipeline comes with documentation about the pipeline, found in the docs/ directory:

  1. Installation
  2. Pipeline configuration
  3. Running the pipeline
  4. Output and how to interpret the results
  5. Troubleshooting

Credits

nf-core/nanodemux was originally written by Chelsea Sawyer and Harshil Patel from The Bioinformatics & Biostatistics Group for use at The Francis Crick Institute, London.

Many thanks to others who have helped out along the way too, including (but not limited to): @crickbabs

Citation

Ewels PA, Peltzer A, Fillinger S, Alneberg JA, Patel H, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. nf-core: Community curated bioinformatics pipelines. bioRxiv. 2019. p. 610741. doi: 10.1101/610741.