Summary QC statistics
- Samples number: 8
- Final samples number post-DADA2: 8
- Missing samples (Not enough reads, do not pass QC, etc):
- Total number of CCS reads before filtering and primers trimming:
107538
- Was primers trimmed prior to DADA2? Yes
- Total number of reads after quality filtering: 107459 (99.93%)
- Total number of reads after primers trimming (DADA2 input): 106005
(98.65%)
- Total number of ASVs found: 53
- Average number of ASVs per sample: 47
- Total number of reads in 53 ASVs: 89413 (84.35% of all input
reads)
Classification using VSEARCH with a single database
- ASVs classified at Species level: 53 (100%)
- ASVs classified at Species level (Excluding metagenome/uncultured
entries): 53 (100%)
- Percentage reads belong to ASV classified at Species level
(Excluding metagenome/uncultured entries): 100%
- ASVs classified at Genus level: 53 (100%)
- ASVs classified at Genus level (Excluding metagenome/uncultured
entries): 53 (100%)
- Percentage reads belong to ASV classified at Genus level (Excluding
metagenome/uncultured entries): 100%
Classification using Naive Bayes classifier with SILVA, GTDB and
RefSeq + RDP
- ASVs classified at Species level: 50 (94.34%)
- ASVs classified at Species level (Excluding metagenome/uncultured
entries): 50 (94.34%)
- Percentage reads belong to ASV classified at Species level
(Excluding metagenome/uncultured entries): 91%
- ASVs classified at Genus level: 53 (100%)
- ASVs classified at Genus level (Excluding metagenome/uncultured
entries): 53 (100%)
- Percentage reads belong to ASV classified at Genus level (Excluding
metagenome/uncultured entries): 100%
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 rarefecation 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.
