Sequence statistics of studies included in the meta-analysis
| Study acronym | Raw seq counts | Avg read len (±SD) | Biospecimen processed through QIIME-CR | Biospecimen processed through SS-UP | Avg Reads/biospecimen reported in manuscript | Fraction of raw reads assigned to OTUs (QIIME-CR) (%) | Fraction of raw reads assigned to OTUs (SS-UP) (%) | Avg reads±SD QIIME-CR | Avg reads±SD SS-UP |
|---|---|---|---|---|---|---|---|---|---|
| Wang_V3_454 | 347 716 | 186.4±34.9 | 102 | 102 | 2734±460 | 81.1 | 92.2 | 2763.7±456.8 | 2811.5±463.1 |
| Chen_V13_454 | 508 160 | 444.2±145.8 | 42 | 42 | 4253 | 26.4 | 64.7 | 3190.5±617.6 | 3756.7±579.7 |
| Wu_V3_454 | 1 076 196 | 180.4±46.9 | 31 | 31 | 18,522 | 53.1 | 75.5 | 18430.2±10572.5 | 17886.4±10602.3 |
| Weir_V4_454 | 199 750 | 250.9±99.6 | 13 | 13 | 1250 | 6.2 | 81.2 | 688.3±1317.6 | 2641.7±5142.7 |
| Brim_V13_454 | 700 890 | 416.6±149.4 | 12 | 12 | NA | 66.5 | 81.3 | 38854.4±7935.2 | 40362.17±8006.3 |
| Zackular_V4_MiSeq | 11 243 169 | 252.9±1.4 | 90 | 90 | Median :95,464 | 81.9 | 96.2 | 109664.5±56565.3 | 128029.4±67747.5 |
| Zeller_V4_MiSeq | 43 461 917 | 254.5±13.8 | 129 | 129 | NA | 85.4 | 81.7 | 287613.4±159160.3 | 293229.5±162297.9 |
| Pascual_V13_454 | 58 850 | 326.2±76.2 | 28 | 28 | 3494 | 39.4 | 92.1 | 1008.7±1058.3 | 2358±5 2567.5 |
| Flemer_V34_MiSeq | 1 567 117 | 448.0±10.3 | 80 | 80 | NA | 45.5 | 86.1 | 8909.7±3204.1 | 16866.0±5582.5 |
Avg reads±SD per sample is reported for each pipeline.
Avg, average; OTUs, operational taxonomic units; QIIME-CR, QIIME closed reference OTU picking; SD, standard deviation; seq, sequence; SS-UP, Strain Select, UPARSE bioinformatics pipeline.