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:
75041449
- 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 (4.26%)
- Total number of reads after primers trimming (DADA2 input): 3197382
(99.92%)
- Total number of ASVs found: 2222
- Average number of ASVs per sample: 483
- Total number of reads in 2222 ASVs: 3169977 (99.14% of all input
reads)
Classification using VSEARCH with a single database
- ASVs classified at Species level: 1791 (80.6%)
- ASVs classified at Species level (Excluding metagenome/uncultured
entries): 1791 (80.6%)
- Percentage reads belong to ASV classified at Species level
(Excluding metagenome/uncultured entries): 98%
- ASVs classified at Genus level: 1796 (80.83%)
- ASVs classified at Genus level (Excluding metagenome/uncultured
entries): 1796 (80.83%)
- 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: 1745 (78.53%)
- ASVs classified at Species level (Excluding metagenome/uncultured
entries): 1745 (78.53%)
- Percentage reads belong to ASV classified at Species level
(Excluding metagenome/uncultured entries): 93%
- ASVs classified at Genus level: 1876 (84.43%)
- ASVs classified at Genus level (Excluding metagenome/uncultured
entries): 1865 (83.93%)
- 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.
