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.
- Basecalling, barcoding and adapter trimming (
- FastQ QC (
- Alignment (
.samto co-ordinate sorted
.bamand obtain mapping metrics (
- Present QC for alignment results (
The nf-core/nanodemux pipeline comes with documentation about the pipeline, found in the
- Pipeline configuration
- Running the pipeline
- Output and how to interpret the results
Many thanks to others who have helped out along the way too, including (but not limited to):
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.