Skip to content

Outputs

Reports

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.

Quality control

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

Per-sample outputs

SampleID
  • name_of_pipeline_run.usearch_global.tsv - the Number of reads mapping against each respective OTU, per sample
  • name_of_pipeline_run.precluster.fasta - the final set of OTUs in FASTA format
vsearch

This folder contains the various intermediate processing outputs and is mostly there for debugging purposes.

Pipeline run metrics

pipeline_info

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.html - chronological report of compute tasks and their duration
  • pipeline_trace.txt - Detailed trace log of all processes and their various metrics