Introduction Usage Parameters Output Releases

Introduction

This document describes the output produced by the pipeline. Most of the plots are taken from the MultiQC report, which summarises results at the end of the pipeline.

The directories listed below will be created in the results directory after the pipeline has finished. All paths are relative to the top-level results directory.

Pipeline overview

The pipeline is built using Nextflow and processes data using the following steps:

FastQC

FastQC gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences.

For further reading and documentation see the FastQC help pages.

NB: The FastQC plots displayed in the MultiQC report shows untrimmed reads. They may contain adapter sequence and potentially regions with low quality. To see how your reads look after trimming, look at the FastQC reports in the fastp directory.

Output files:

  • fastqc/
    • *_fastqc.html: FastQC report containing quality metrics for your untrimmed raw fastq files.
  • fastqc/zips/
    • *_fastqc.zip: Zip archive containing the FastQC report, tab-delimited data file and plot images.

NB: The FastQC plots displayed in the MultiQC report shows untrimmed reads. They may contain adapter sequence and potentially regions with low quality.

Sourmash Sketch

Sourmash is a tool to compute MinHash sketches on nucleotide (DNA/RNA) and protein sequences. It allows for fast comparisons of sequences based on their nucleotide content.

Output directory: results/sourmash/sketches

For each sample and provided molecules, ksizes and sketch_num_hashes_log2, a file is created:

  • sample_molecule-${molecule}__ksize-${ksize}__${sketch_value}__track_abundance-${track_abundance}.sig

For example:

SRR4050379_molecule-dayhoff_ksize-3_sketch_num_hashes_log2-2.sig
SRR4050379_molecule-dayhoff_ksize-3_sketch_num_hashes_log2-4.sig
SRR4050379_molecule-dayhoff_ksize-9_sketch_num_hashes_log2-2.sig
SRR4050379_molecule-dayhoff_ksize-9_sketch_num_hashes_log2-4.sig
SRR4050379_molecule-dna_ksize-3_sketch_num_hashes_log2-2.sig
SRR4050379_molecule-dna_ksize-3_sketch_num_hashes_log2-4.sig
SRR4050379_molecule-dna_ksize-9_sketch_num_hashes_log2-2.sig
SRR4050379_molecule-dna_ksize-9_sketch_num_hashes_log2-4.sig
SRR4050379_molecule-protein_ksize-3_sketch_num_hashes_log2-2.sig
SRR4050379_molecule-protein_ksize-3_sketch_num_hashes_log2-4.sig
SRR4050379_molecule-protein_ksize-9_sketch_num_hashes_log2-2.sig
SRR4050379_molecule-protein_ksize-9_sketch_num_hashes_log2-4.sig

Sourmash Compare

Output directory: results/compare_sketches

For each provided molecules, ksizes and sketch_num_hashes_log2, a file is created containing a symmetric matrix of the similarity between all samples, written as a comma-separated variable file:

  • similarities_molecule-${molecule}__ksize-${ksize}__${sketch_value}__track_abundance-${track_abundance}.csv For example,
similarities_molecule-dna_ksize-9_sketch_num_hashes_log2-4.csv
similarities_molecule-protein_ksize-3_sketch_num_hashes_log2-2.csv
similarities_molecule-protein_ksize-3_sketch_num_hashes_log2-4.csv
similarities_molecule-protein_ksize-9_sketch_num_hashes_log2-2.csv
similarities_molecule-protein_ksize-9_sketch_num_hashes_log2-4.csv

MultiQC

MultiQC is a visualization tool that generates a single HTML report summarizing all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in the report data directory.

The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability.

For more information about how to use MultiQC reports, see https://multiqc.info.

Output files:

  • multiqc/
    • multiqc_report.html: a standalone HTML file that can be viewed in your web browser.
    • multiqc_data/: directory containing parsed statistics from the different tools used in the pipeline.
    • multiqc_plots/: directory containing static images from the report in various formats.

Pipeline information

Nextflow provides excellent functionality for generating various reports relevant to the running and execution of the pipeline. This will allow you to troubleshoot errors with the running of the pipeline, and also provide you with other information such as launch commands, run times and resource usage.

Output files:

  • pipeline_info/
    • Reports generated by Nextflow: execution_report.html, execution_timeline.html, execution_trace.txt and pipeline_dag.dot/pipeline_dag.svg.
    • Reports generated by the pipeline: pipeline_report.html, pipeline_report.txt and software_versions.csv.
    • Documentation for interpretation of results in HTML format: results_description.html.
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