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Outputs

Reports

  • name_of_pipeline_run.xlsx: A table with accumulated results - one row per sample per taxon:
Sample Taxon Percentage
SampleA Sus scrofa 75.0
SampleA Bos taurus 25.0
  • name_of_pipeline_run_krona.html: A multi-sample Krona report to visualize taxonomic composition of samples.

krona

The Krona report displays the taxonomic composition of a given as a circular plot, divided into levels of taxonomy.

  • name_of_pipeline_run.html: A graphical and interactive report of various QC steps and results

summary

The summary report contains a variety of information about QC measures as well as the final results. Some of the key metrics are shown at the top, in the section labelled Summary. The status column aims to highlight the overall quality of a given sample, although users are advised to develop their own relevant cutoff metrics for the various processing stages, such as a minimum number of reads required after clustering for a sample to be considered for analysis, or the maximum amount of chimeric reads that are tolerated for a particular application.

Per-sample outputs

Sample-level reports can be found in the folder results/samples/sample_id.

When using Vsearch for OTU clustering - vsearch/sample_id.usearch_global.tsv: the number of reads mapping against each respective OTU, per sample - vsearch/sample_id.precluster.fasta: the final set of OTUs in FASTA format

When using DADA2 for OTU/ASV clustering - DADA2/sample_id_ASVs.fasta: the clustered sequences (OTU/ASV)

That same folder also contains a number of additional metrics and outputs, including graphical summaries of the error profiles that can be used to debug sample-specific issues.

  • blast/sample_id.filtered.json: JSON listing of all BLAST hits
  • blast/sample_id.consensus.json: JSON listing of consensus taxa assigned to each sequence cluster

This folder contains some of the raw sample-level outputs.

  • report/sample_id.composition.tsv: the taxonomic composition of this sample in TSV format.
  • report/sample_id.composition.json: the taxonomic composition of this sample in JSON format.
  • report/sample_id.blast_stats.tsv: Details of the blast matches against each respective OTU.
  • report/sample_id.report.json: A JSON summary of the results and QC for this sample

Pipeline run metrics

This folder contains the pipeline run metrics

  • pipeline_dag.svg: the workflow graph (only available if GraphViz is installed)
  • pipeline_report.html: the (graphical) summary of all completed tasks and their resource usage
  • pipeline_report.txt: a short summary of this analysis run in text format
  • pipeline_timeline.htm: chronological report of compute tasks and their duration
  • pipeline_trace.txt: Detailed trace log of all processes and their various metrics