Table 2.
Target yield depending on the sequencing strategy/targeted genomics analysis.
| SAMPLE MATERIAL | SAMPLE PROTOCOL | Metagenomics | 16S metabarcoding | 18S metabarcoding | ITS2 metabarcoding | Metatranscriptomics on PROK RNA | Metatranscriptomics on EUK RNA | Metaviromics |
|---|---|---|---|---|---|---|---|---|
| MARINE MICROBIOME | S300 (>300 µm) | 100 M seq | 0.5–1 M seq | 0.3–0.5 M seq | 100 M seq | |||
| 2 × 150 bp | 2 × 250 bp | 2 × 150 bp | 2 × 150 bp | |||||
| HiSeq 4000 (2017) | HiSeq 2500 R (2016–2019) | HiSeq 2500 R (2016–2018) | HiSeq 4000 (2016–2018) | |||||
| NovaSeq 6000 S4 (2018–2019) | MiSeq (2019) | MiSeq (2018–2019) | NovaSeq 6000 S2 (2018) | |||||
| NovaSeq 6000 SP (2019) | HiSeq 4000 (2016–2018) | NovaSeq 6000 S4 (2018) | ||||||
| NovaSeq 6000 SP (2019) | ||||||||
| S20 (>20 µm) | 100 M seq | 0.5–1 M seq | 0.3–0.5 M seq | 100 M seq | ||||
| 2 × 150 bp | 2 × 250 bp | 2 × 150 bp | 2 × 150 bp | |||||
| HiSeq 4000 (2017) | HiSeq 2500 R (2016–2019) | HiSeq 2500 R (2016–2018) | HiSeq 2500 R (2016) | |||||
| NovaSeq 6000 S4 (2018–2020) | MiSeq (2019–2020) | MiSeq (2018–2019) | HiSeq 4000 (2016–2018) | |||||
| NovaSeq 6000 SP (2019–2020) | HiSeq 4000 (2016–2018) | NovaSeq 6000 S4 (2018) | ||||||
| NovaSeq 6000 SP (2019) | ||||||||
| S320 (3–20 µm) | 100 M seq | 0.5–1 M seq | 0.3–0.5 M seq | 20 000 seq | 100 M seq | |||
| S3 = (>3 µm) | 2 × 150 bp | 2 × 250 bp | 2 × 150 bp | 2 × 250 bp | 2 × 150 bp | |||
| HiSeq 4000 (2017–2018) | HiSeq 2500 R (2016–2019) | HiSeq 2500 R (2016–2018) | HiSeq 2500 R (2016) | HiSeq 4000 (2016–2018) | ||||
| NovaSeq 6000 S4 (2018–2020) | MiSeq (2018–2019) | MiSeq (2018–2019) | MiSeq (2017–2019) | NovaSeq 6000 S2 (2018) | ||||
| NovaSeq 6000 SP (2019–2020) | HiSeq 4000 (2016–2018) | NovaSeq 6000 S4 (2018–2020) | ||||||
| NovaSeq 6000 SP (2019) | ||||||||
| S023 (0.2–3 µm) | 100 M seq | 0.5–1 M seq | 0.3–0.5 M seq | 100 M seq | 100 M seq | |||
| 2 × 150 bp | 2 × 250 bp | 2 × 150 bp | 2 × 150 bp | 2 × 150 bp | ||||
| HiSeq 4000 (2016–2018) | HiSeq 2500 R (2016–2019) | HiSeq 2500 R (2016) | HiSeq 4000 (2016–2018) | HiSeq 4000 (2016–2018) | ||||
| NovaSeq 6000 S4 (2018–2019) | MiSeq (2019–2020) | MiSeq (2018–2019) | NovaSeq 6000 S4 (2018–2020) | NovaSeq 6000 S4 (2018–2020) | ||||
| NovaSeq 6000 SP (2019–2020) | HiSeq 4000 (2016–2018) | |||||||
| NovaSeq 6000 SP (2019) | ||||||||
| S<02 (<0.2 µm) | 100 M seq | |||||||
| 2 × 150 bp | ||||||||
| HiSeq 4000 (2017–2018) | ||||||||
| NovaSeq 6000 S1 (2019 | ||||||||
| CORAL HOLOBIONT | CS4L | 100 M seq | 0.5–1 M seq | 0.1 M seq | 20 000 seq | 40 M seq | ||
| (Pocillopora-Porites-Millepora) | 2 × 150 bp | 2 × 250 bp | 2 × 150 bp | 2 × 250 bp | 2 × 150 bp | |||
| HiSeq 4000 (2016–2020) | HiSeq 2500 R (2018) | HiSeq 2500 R (2017–2019) | HiSeq 2500 R (2017–2019) | HiSeq 2500 R (2016) | ||||
| NovaSeq 6000 S4 (2020) | MiSeq (2019) | HiSeq 4000 (2106–2018) | MiSeq (2017–2019) | MiSeq (2017) | ||||
| NovaSeq 6000 SP (2019) | MiSeq (2107–2019) | HiSeq 4000 (2017–2019) | ||||||
| NovaSeq 6000 SP (2019) | NovaSeq 6000 S2 (2018) | |||||||
| NovaSeq 6000 S4 (2018–2019) | ||||||||
| CDIV | 0.5–1 M seq | 0.1 M seq | 20 000 seq | |||||
| (diverse coral species) | 2 × 250 bp | 2 × 150 bp | 2 × 250 bp | |||||
| NovaSeq 6000 SP (2019) | NovaSeq 6000 SP (2019) | MiSeq (2019) | ||||||
| FISH | GT (Gut tissue) | 40 M seq | 0.5–1 M seq | |||||
| 2 × 150 bp | 2 × 250 bp | |||||||
| HiSeq 2500 R (2016) | HiSeq 2500 R (2017–2018) | |||||||
| HiSeq 4000 (2017–2018) | MiSeq (2018–2019) | |||||||
| NovaSeq 6000 S4 (2019–2020) | NovaSeq 6000 SP (2019) | |||||||
| MUC (Mucus tissue) | 0.5–1 M seq | |||||||
| 2 × 250 bp | ||||||||
| HiSeq 2500 R (2018) | ||||||||
| MiSeq (2018–2019) | ||||||||
| NovaSeq 6000 SP (2019) | ||||||||
| AEROSOLS | AS-ABS | 0.5–1 M seq | ||||||
| 2 × 250 bp | ||||||||
| HiSeq 2500 R (2019) | ||||||||
| MiSeq (2018–2019) | ||||||||
| SEDIMENT | SSED | 0.5–1 M seq | 0.3–0.5 M seq | 20 000 seq | ||||
| 2 × 250 bp | 2 × 150 bp | 2 × 250 bp | ||||||
| HiSeq 2500 R (2019–2020) | HiSeq 2500 R (2019) | MiSeq (2019) | ||||||
| NovaSeq 6000 SP (2020) | NovaSeq 6000 SP (2019) |