NXF - TGS Oxford Nanopore pipeline

Process raw Oxford Nanopore data, generate html report, and do de novo assembly (plasmid, amplicon, bacterial genome)

About

Nextflow pipeline for processing raw Oxford Nanopore run data - merge/rename files, generate read reports, run ONT workflows (wf-clone-validation, wf-bacterial-genomes or wf-amplicon). Raw reads are mapped back to the assemblies and the alignments are visualised in IGV html reports. This pipeline can also be imported and run in EPI2ME.

Running

Only nextflow and docker are required. The required inputs for the pipeline are:

--samplesheet - path to a csv or excel file with columns sample, barcode and user. Other columns can also be there.
--fastq - path to fastq_pass

The pipelines runs the following steps:

merge_reads - merge all reads belonging to a barcode and rename according to the provided samplesheet
report - generate a csv and html reports about read counts, quality etc. One report per user is generated.
assembly - perform assembly using one of the epi2me pipelines wf-clone-validation, wf-bacterial-genomes or wf-amplicon (default wf-clone-validation)
mapping and IGV - map raw reads to the assemblies and generate html IGV reports (one report per sample).

nextflow run angelovangel/nxf-tgs --samplesheet path/to/samplesheet.csv --fastq path/to/fastq_pass

It is possible to run only merge_reads or merge_reads + report. For this, use the -entry parameter (note the single dash) in nextflow like so:

nextflow run angelovangel/nxf-tgs --samplesheet path/to/samplesheet.csv --fastq path/to/fastq_pass -entry report

This will run merge_reads + report and no asembly and mapping...

Run in EPI2ME

You can import and run the pipeline using GUI in EPI2ME. There is also a test dataset to try if all works - after importing select 'Options' --> 'Run demo analysis'.