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:

BlobDir

The files in the BlobDir dataset which is used to create the online interactive assessments.

Output files
  • blobtoolkit/
    • <assembly>/
      • *.json.gz: files generated from genome and alignment coverage statistics.

More information about visualising the data in the BlobToolKit repository

Static plots

Images generated from the above blobdir using the blobtk tool.

Output files
  • blobtoolkit/
    • plots/
      • <assembly>.*.png or <assembly>.*.svg, depending on the selected output format: static versions of the BlobToolKit plots.

BUSCO

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

Output files
  • busco/
    • <lineage>/
      • <assembly>.<lineage>.short_summary.json: BUSCO scores for that lineage as JSON.
      • <assembly>.<lineage>.short_summary.tsv: BUSCO scores for that lineage as a tab-separated file (not for pre-computed BUSCOs).
      • <assembly>.<lineage>.short_summary.txt: BUSCO scores for that lineage as formatted text.
      • <assembly>.<lineage>.full_table.tsv: Coordinates of the annotated BUSCO genes as a tab-separated file.
      • <assembly>.<lineage>.missing_busco_list.tsv: List of the BUSCO genes that could not be found.
      • <assembly>.<lineage>.<single_copy>_busco_sequences.tar.gz: Sequence archives of the annotated BUSCO genes.

Repeat masking

Results from the repeat-masker step -- only if the pipeline is run with --mask.

Output files
  • repeats/
    • windowmasker/
      • <assembly>.fasta: masked assembly in FASTA format.
      • <assembly>.obinary: frequency counts of repeats, in windowmasker's own binary format.

Read alignments

Read alignments in BAM format -- only if the pipeline is run with --align.

Output files
  • read_mapping/
    • <datatype>/
      • <sample>/ (can be nested directories if sample contains /)
        • <assembly>.<datatype>.<sample>.minimap2.bam: alignments of that sample's reads in BAM format. (/ in the sample name are replaced with .)
        • <assembly>.<datatype>.<sample>.minimap2.bam.csi: index of the BAM file. (/ in the sample name are replaced with .)

Read coverage

Read coverage statistics as computed by the pipeline. Those files are the raw data used to build the BlobDir. The <window_size> is formatted as <N>k when the window size is divisible by 1000 (for example 1k) and <N>bp otherwise (for example 1500bp).

Output files
  • read_mapping/
    • <datatype>/
      • <sample>/ (can be nested directories if sample contains /)
        • <assembly>.<datatype>.<sample>.coverage.<window_size>.bed.gz: BedGraph file with per-window coverage. (/ in the sample name are replaced with .)
        • <assembly>.<datatype>.<sample>.minimap2.coverage.<window_size>.bed.gz: same as above when alignments are generated by this pipeline using minimap2 (--align). (/ in the sample name are replaced with .)

Base content

k-mer statistics. Those files are the raw data used to build the BlobDir. The <window_size> follows the same formatting as in Read coverage.

Output files
  • base_content/
    • k1/, k2/, k3/, k4/
      • <assembly>.<mono>.<window_size>.tsv.gz: tab-separated files with counts of every k-mer for k ≤ 4. The first three columns correspond to the coordinates (sequence name, start, end), followed by each k-mer.
    • <assembly>.freq.<window_size>.tsv.gz: tab-separated file with frequencies derived from the k-mer counts.

MultiQC report

Output files
  • multiqc_report.html: Interactive HTML report summarizing quality metrics from BUSCO.

Resources / databases

Output files
  • resources/
    • new_taxdump.json: Input NCBI taxonomy digested into a JSON file. Can be used to speed up further runs of the pipeline.

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 parameters are used when running the pipeline.
    • Reformatted samplesheet files used as input to the pipeline: samplesheet.valid.csv.
    • Parameters used by the pipeline run: params.json.

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.