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

Per-sample outputs

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