Quality Control

Before proceeding to diversity analyses, we inspect our sequencing controls to evaluate potential contamination, assess reagent blanks, and confirm our negative controls behave as expected.

Summarize the Filtered Table

Get a per-sample read count summary of the contaminant-filtered table:

qiime feature-table summarize \
  --i-table table_nomitochloro.qza \
  --o-visualization table_nomitochloro.qzv \
  --m-sample-metadata-file metadata_q2_workshop.txt

Use this visualization to work through the following checklist:

Table Summary Review Reset

Identify samples with very low read countsThese may need to be excluded before diversity analysis Determine a minimum read count thresholdUsed for downstream sample filtering Choose a rarefaction depthSee the Rarefaction page for guidance

Filter to Control Samples Only

Isolate sequencing controls (e.g., extraction blanks, PCR negatives) using a metadata-based filter:

qiime feature-table filter-samples \
  --i-table table.qza \
  --m-metadata-file metadata_q2_workshop.txt \
  --p-where "[sample_type]='control'" \
  --o-filtered-table table_controls.qza

Visualize Control Taxonomy

qiime taxa barplot \
  --i-table table_controls.qza \
  --i-taxonomy taxonomy_gg2.qza \
  --m-metadata-file metadata_q2_workshop.txt \
  --o-visualization taxa_barplot_controls.qzv

When you open taxa_barplot_controls.qzv, work through this checklist:

Control Interpretation Reset

Negative controls have very few reads overallHigh read counts in controls suggest contamination No taxa are highly abundant in both controls and soil samplesOverlap may indicate reagent or extraction contamination Any suspect taxa flagged for investigationResolve before proceeding to diversity analyses

Outputs

File	Type	Description
table_nomitochloro.qzv	Visualization	Per-sample read count summary
table_controls.qza	Artifact	Feature table filtered to controls only
taxa_barplot_controls.qzv	Visualization	Taxonomic composition of controls

Next: Rarefaction