ToulligQC Workflow

A post sequencing QC tool for Oxford Nanopore sequencers

Introduction

ToulligQC is dedicated to the QC analyses of Oxford Nanopore runs, and it is adapted to RNA-Seq along with DNA-Seq.
This QC tool supports only Guppy and Dorado basecalling ouput files. It also needs a single FAST5 file (to catch the flowcell ID and the run date) if a telemetry file is not provided.
Flow cells and kits version are retrieved using the telemetry file. ToulligQC can take barcoding samples by adding the barcode list as a command line option.

If the sequencing summary file is not available, ToulligQC can also accept FASTQ or BAM files.

To do so, ToulligQC deals with different file formats: gz, tar.gz, bz2, tar.bz2 and .fast5 to retrieve a FAST5 information. This tool will produce a set of graphs, statistic file in plain text format and a HTML report.

To run ToulligQC you need the Guppy/ Dorado basecaller output files : sequencing_summary.txt and sequencing_telemetry.js. or FASTQ or BAM This can be compressed with gzip or bzip2. You can use your initial Fast5 ONT file too. ToulligQC can perform analyses on your data if the directory is organised as the following:

Quickstart

The workflow uses nextflow to manage compute and software resources, as such nextflow will need to be installed before attempting to run the workflow.

The workflow can currently be run using either Docker or Singularity to provide isolation of the required software. Both methods are automated out-of-the-box provided either Docker or Singularity is installed.

It is not required to clone or download the git repository in order to run the workflow. For more information on running EPI2ME Labs workflows visit out website.

Workflow options

To obtain the workflow, having installed nextflow, users can run:

nextflow run epi2me-labs/wf-template --help

to see the options for the workflow.

Input parameters

Input Options

Nextflow parameter name	Type	Description	Help	Default
sequencing_summary_source	string	Basecaller sequencing summary source, can be compressed with gzip (.gz) or bzip2 (.bz2)
barcoding_summary_pass	string	Basecaller barcoding summary source of passed reads, can be compressed with gzip (.gz) or bzip2 (.bz2).
barcoding_summary_fail	string	Basecaller barcoding summary source of passed reads, can be compressed with gzip (.gz) or bzip2 (.bz2).
telemetry_source	string	Basecaller telemetry file source, can be compressed with gzip (.gz) or bzip2 (.bz2)
fast5	string	Fast5 file source, can also be in a tar.gz/tar.bz2 archive or a directory	Necessary if no telemetry file
fastq	string	FASTQ files to use in the analysis, can also be in a .gz archive	Necessary if no sequencing summary file
bam	string	BAM or SAM files to use in the analysis, can also be a SAM format.	Necessary if no sequencing summary file
barcoding	boolean	BAM or SAM files to use in the analysis.		False
barcodes	string	Coma separated barcode list (e.g. BC05,RB09,NB01,barcode10)	ToulligQC handle the following naming schemes: BCXX, RBXX, NBXX and barcodeXX where XX is the number of the barcode

Sample Options

Nextflow parameter name	Type	Description	Help	Default
report_name	string	Name to give to report

Miscellaneous Options

Nextflow parameter name	Type	Description	Help	Default
disable_ping	boolean	Enable to prevent sending a workflow ping.		False

Workflow outputs

Title	File path	Description	Per sample or aggregated
workflow report	./wf-template-report.html	Report for all samples.	aggregated

Useful links

• nextflow
• docker
• singularity