Table 4. Read tracking information and OTU/ASV outputs for the pipeline flows applied to the HELIUS data.
| Pipeline Flow | Merged [% of raw] | Filtered [% of raw] | Clustered / Denoised [% of raw] | Conversion to OTUs/ASVs [% of filtered] | Conversion to OTUs/ASVs [% of raw] | Total no. of OTUs/ASVs | Non-singleton OTUs / ASVs | Singleton OTUs / ASV |
|---|---|---|---|---|---|---|---|---|
| OTU-level | ||||||||
| QIIME-uclust (default) | 86.78 | 86.78 | 86.78 | 99.57 | 86.41 | 201735 | 201735 | 0 |
| QIIME-uclust (Q20) | 86.78 | 86.41 | 86.41 | 99.66 | 86.12 | 195377 | 195377 | 0 |
| QIIME-uclust (e30.ee1) | 93.01 | 82.90 | 82.90 | 99.91 | 82.82 | 150752 | 150752 | 0 |
| MOTHUR (DGC.0) | 70.48 | 66.37 | 94.17 | 66.37 | 23347 | 16161 | 7186 | |
| MOTHUR (DGC.1) | 70.48 | 66.39 | 94.19 | 66.39 | 12822 | 12640 | 182 | |
| MOTHUR (DGC.3) | 70.48 | 65.47 | 92.89 | 65.47 | 4022 | 3832 | 190 | |
| MOTHUR (Opticlust.3) | 70.48 | 65.47 | 92.89 | 65.47 | 5302 | 5053 | 249 | |
| USEARCH-UPARSE | 93.01 | 82.90 | 82.90 | 96.60 | 89.85 | 5559 | 5557 | 0 |
| ASV-level | ||||||||
| DADA2 (ee2) | 73.82 | 71.26 | 95.00 | 70.13 | 26763 | 26763 | 0 | |
| DADA2 (no filter) | 98.12 | 90.11 | 90.45 | 88.75 | 24469 | 24469 | 0 | |
| Qiime2-Deblur (default) | 74.53 | 74.53 | 74.53 | 51.50 | 38.39 | 11120 | 11120 | 0 |
| Qiime2-Deblur (Q20) | 74.53 | 74.53 | 74.53 | 51.50 | 38.38 | 11120 | 11120 | 0 |
| Qiime2-Deblur (e30.ee1) | 93.01 | 82.90 | 82.90 | 51.04 | 42.31 | 11735 | 11735 | 0 |
| USEARCH-UNOISE3 | 93.01 | 82.90 | 82.90 | 97.48 | 90.67 | 7659 | 7519 | 140 |