Summary QC statistics
- Samples number: 32
- Final samples number post-DADA2: 32
- Missing samples (Not enough reads, do not pass QC, etc):
- Total number of CCS reads before filtering and primers trimming:
33300804
- Was primers trimmed prior to DADA2? Yes
- Note that if downsampling was enabled, the reads will be filtered
first, then restricted to a maximum of N reads.
- Total number of reads after quality filtering: 3200000 (9.61%)
- Total number of reads after primers trimming (DADA2 input): 3197210
(99.91%)
- Total number of ASVs found: 2043
- Average number of ASVs per sample: 424
- Total number of reads in 2043 ASVs: 3168432 (99.1% of all input
reads)
Classification using VSEARCH with a single database
- ASVs classified at Species level: 1659 (81.2%)
- ASVs classified at Species level (Excluding metagenome/uncultured
entries): 1659 (81.2%)
- Percentage reads belong to ASV classified at Species level
(Excluding metagenome/uncultured entries): 98%
- ASVs classified at Genus level: 1663 (81.4%)
- ASVs classified at Genus level (Excluding metagenome/uncultured
entries): 1663 (81.4%)
- Percentage reads belong to ASV classified at Genus level (Excluding
metagenome/uncultured entries): 98%
Classification using Naive Bayes classifier with SILVA, GTDB and
RefSeq + RDP
- ASVs classified at Species level: 1611 (78.85%)
- ASVs classified at Species level (Excluding metagenome/uncultured
entries): 1611 (78.85%)
- Percentage reads belong to ASV classified at Species level
(Excluding metagenome/uncultured entries): 90%
- ASVs classified at Genus level: 1732 (84.78%)
- ASVs classified at Genus level (Excluding metagenome/uncultured
entries): 1721 (84.24%)
- Percentage reads belong to ASV classified at Genus level (Excluding
metagenome/uncultured entries): 96%
Overall reads filtering and number of full-length reads
- Full-length reads are defined as reads with both F27 and R1492
primers
- Note that full length counts column will only show if cutadapt was
used to trim primers (default).
DADA2 QC metrics
Top Taxa and Plots
- For interactive view, use the Emperor QZV output from QIIME2 in
results/core-metrics-diversity folder with QIIME2 View
- Note that if the distances between all samples are zero for a
specific method, the plots will not be shown.
- MDS plots use ASVs as input.
- Samples might be missing due to choice of rarefecation depth. Rerun
pipeline with
-resume --rarefaction_depth X to choose a
custom rarefaction depth X.
Bray-Curtis MDS plot
Weighted and Unweighted Unifrac MDS plot
Top 50 ASVs (VSEARCH classification)
Top 10 Classified Genus (Collapsed to species) with VSEARCH
- Relative abundance is calculated by dividing the number of reads for
each ASV to the total number of reads in each sample.
- Heatmap contains only species with >1% abundance in at least 2
samples for the top 10 genus.
Top 50 ASVs (Naive Bayes Classifier)
Top 10 Classified Genus (Collapsed to species) with Naive Bayes
Classifier
- Relative abundance is calculated by dividing the number of reads for
each ASV to the total number of reads in each sample.
- Heatmap contains only species with >1% abundance in at least 2
samples for the top 10 genus.
