dalmolingroup/euryale: Output

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 (steps in italics don't run by default):

  • Kaiju and/or Kraken2 - Taxonomically classify reads or contigs
  • Krona - Visualize the taxonomic classification for each sample.
  • MicroView - Visualize the taxonomic diversity for each sample.
  • Diamond - Alignment reads and contigs against a reference database (such as NCBI-nr).
  • Annotate - Functional annotation of alignment matches.
  • MEGAHIT - Assembled contigs.
  • MultiQC - Aggregate report describing results and QC from the whole pipeline
  • Pipeline information - Report metrics generated during the workflow execution

Kaiju and Kraken2

Output files - `taxonomy/${sample}/` - `${sample}.tsv`: Classification output. - `${sample}.txt`: Kaiju2Table TSV output.

Kaiju is a software to perform fast taxonomic classification of metagenomic sequencing reads using a protein reference database.

Kraken2 is the second version of the Kraken taxonomic sequence classification system.

Krona

Output files - `taxonomy/${sample}/` - `${sample}.html`: Krona visualization for the sample.
  • Krona is a tool to interactively explore metagenomes and more from a web browser.

MicroView

Output files - `taxonomy/microview/` - `microview_report.html`: MicroView report for all samples. - `microview_tables/`: Tables used for the MicroView visualizations.
  • MicroView is a reporting tool for aggregating results from taxonomic classification analyses.

Diamond

Output files - `alignment/${sample}/` - `${sample}.txt`: Alignment matches in blast tabular output format. - `${sample}.log`: DIAMOND execution log.
  • DIAMOND is an accelerated BLAST compatible local sequence aligner.

Annotate

Output files - `functional/${sample}/` - `${sample}_annotated.txt`: Alignment matches annotated to chosen functional database (e.g. GO).
  • Annotate is a tool to annotate each query using the best alignment for which a mapping is known.

MEGAHIT

Output files - `assembly/${sample}/` - `${sample}.contigs.fa.gz`: Contigs assembled for the sample.
  • MEGAHIT is an ultra-fast and memory-efficient (meta-)genome assembler

DIAMOND database

Output files - `diamond_db/` - `${database_name}.dmnd`: DIAMOND database for the reference fasta file.

  • This output is present if you add the --save_db parameter.

  • DIAMOND is an accelerated BLAST compatible local sequence aligner.

MultiQC

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.

MultiQC is a visualization tool that generates a single HTML report summarising 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.

Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. 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 http://multiqc.info.

Pipeline information

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.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline. - Reformatted samplesheet files used as input to the pipeline: `samplesheet.valid.csv`.

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.