Introduction

This document describes the output produced by 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. The directories comply with Tree of Life's canonical directory structure.

Pipeline overview

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

  • Contact maps – Contact matrix created using HiC sequencing data
  • Genome statistics – Collated assembly information, genome statistics and alignment quality information
  • BUSCO - BUSCO results
  • MultiQC - Aggregate report describing results from the whole pipeline
  • Pipeline information - Report metrics generated during the workflow execution

Contact maps

This pipeline takes aligned HiC reads to create contact maps and chromosomal grid using Cooler for display on a HiGlass server.

Output files
  • contact_maps/
    • <sample>.bedpe: chromosomal grid created from the .cool file
    • <sample>.cool: initial contact matrix created
    • <sample>.mcool: final contact matrix for upload

Genome statistics

This pipeline collates (1) assembly information, statistics and chromosome details from NCBI datasets, (2) genome completeness from BUSCO, (3) consensus quality and k-mer completeness from MerquryFK, and (4) HiC primary mapped percentage from samtools flagstat.

Output files
  • genome_note/
    • <gca_accession>.csv: collate genome statistics file
    • <gca_accession>.{docx|xml}: partially completed genome note template file
    • <gca_accession>_genome_note_consistent.csv: a file of genome metadata parameters pulled from various public data repositories where all source agree on the paramter value.
    • <gca_accession>_genome_note_inconsistent.csv: a file of genome metadata parameters, and their sources pulled from various public data repositories where the paramter value differs between data sources.

BUSCO

BUSCO results generated by the pipeline (all BUSCO lineages that match the claassification of the species).

Output files
  • busco/
    • <lineage_name>
      • short_summary.{json|tsv|txt}: BUSCO scores in various formats.
      • full_table.tsv: list and coordinates of BUSCO genes that could be found
      • missing_busco_list.tsv: BUSCO genes that could not be found
      • {single,multi,fragmented}_busco_sequences.tar.gz: sequence files of the annotated genes.
      • hmmer_output.tar.gz: Scores and outputs from the HMMER searches

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. Some of the pipeline results are visualised in the report and further statistics are available in the report data directory.

Results generated by MultiQC collate pipeline from supported tools e.g. BUSCO. 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/genomenote/
    • 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.