Table 1.
Information on tested datasets
| Method | Property | Dataset |
|||
|---|---|---|---|---|---|
| Extreme | Even1 | Stag1 | Vagina | ||
| NA | Region | V4 | V4 | V4 | V1–V2 |
| Length (nt) | 250 | 250 | 250 | 300 | |
| No. strains | 27 | 21 | 21 | – | |
| No. reads | 2.0M | 1.0M | 1.3M | 2.1M | |
| DADA2 | t (s) | 2252.0 | 1487.6 | 1266.0 | 343.1 |
| Mem (MB) | 12576.8 | 4043.4 | 6137.1 | 2747.3 | |
| Deblur | t (s) | 2211.2 | 708.0 | 937.8 | 1591.2 |
| Mem (MB) | 6658.0 | 1265.4 | 2138.3 | 648 | |
| UNOISE3 | t (s) | 11.7+1.4 (13.1) | 4.2+0.2 (4.4) | 5.7+0.3 (6.0) | 10.4+1.9 (12.3) |
| Mem (MB) | 1245.6 | 671.5 | 926.6 | 1304.6 | |
| AmpliCI | t (s) | 73.0+423.3 (496.3) | 53.7+2738.7 (2792.4) | 72.1+2725.9 (2798.0) | 32.2+133.6 (165.8) |
| Mem (MB) | 3924.5 | 5171.9 | 6884.7 | 64.8 | |
Note: All datasets contain 16S rRNA gene amplicon sequences generated on the Miseq platform. For DADA2 and Deblur: time recorded for the whole workflow. For UNOISE3: time recorded for data compression (-fastx_uniques) and denoising (-unoise3). For AmpliCI: time recorded for error estimation and haplotype inference. Total time in parentheses.
NA, not Applicable; Length (nt), read length in nucleotides; No. strains, number of known strains in mock community; No. reads, total number of reads in dataset; t, running time; mem, maximum resident set size.