HiFi Full-length 16S Analysis Report
Summary QC statistics
- Samples number: 1
- Final samples number post-DADA2: 1
- Missing samples (Not enough reads, do not pass QC, etc):
- Total number of CCS reads before filtering and primers trimming: 2690358
- 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: 100000 (3.72%)
- Total number of reads after primers trimming (DADA2 input): 97308 (97.31%)
- Total number of ASVs found: 1223
- Average number of ASVs per sample: 1223
- Total number of reads in 1223 ASVs: 95264 (97.9% of all input reads)
Classification using VSEARCH with a single database
- ASVs classified at Species level: 989 (80.87%)
- ASVs classified at Species level (Excluding metagenome/uncultured entries): 989 (80.87%)
- Percentage reads belong to ASV classified at Species level (Excluding metagenome/uncultured entries): 93%
- ASVs classified at Genus level: 992 (81.11%)
- ASVs classified at Genus level (Excluding metagenome/uncultured entries): 992 (81.11%)
- Percentage reads belong to ASV classified at Genus level (Excluding metagenome/uncultured entries): 93%
Classification using Naive Bayes classifier with SILVA, GTDB and RefSeq + RDP
- ASVs classified at Species level: 954 (78%)
- ASVs classified at Species level (Excluding metagenome/uncultured
entries): 954 (78%)
- Percentage reads belong to ASV classified at Species level
(Excluding metagenome/uncultured entries): 87%
- ASVs classified at Genus level: 1036 (84.71%)
- ASVs classified at Genus level (Excluding metagenome/uncultured
entries): 1026 (83.89%)
- Percentage reads belong to ASV classified at Genus level (Excluding metagenome/uncultured entries): 91%
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).
Input reads QC (Before filtering and primers removal)
DADA2 QC metrics
Top Taxa and Plots
- For interactive view, use the Emperor QZV output from QIIME2 in
results/core-metrics-diversityfolder 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 Xto choose a custom rarefaction depth X.
Bray-Curtis MDS plot
## [1] "Bray-Curtis matrix is empty (Did you process only one sample?)"Weighted and Unweighted Unifrac MDS plot
## [1] "Weighted unifrac matrix is empty (Did you process only one sample?)"## [1] "Unweighted unifrac matrix is empty (Did you process only one sample?)"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.
