Table 2 Target yield depending on the sequencing strategy/targeted genomics analysis.

From: Integrative omics framework for characterization of coral reef ecosystems from the Tara Pacific expedition

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)

 
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