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Table 1 Summary statistics for all metagenomic libraries used in analysis

From: Sequencing platform and library preparation choices impact viral metagenomes

 

DNA source

Technology

Starting DNA (ng)

Library amplification (# cycles)

Replicates

Raw reads (millions)

Raw quality +/-SD (PHRED)

Raw length (bp)

Failed QC +/- SD (%)

Experiment 1

Biosphere 2 Ocean

Illumina HiSeq 2000

1,000

14

2

65.5, 51.8

34.2 +/- 0.0

100 PE

29.9 +/- 0.5

100

14

2

6.7, 0.3

33.8 +/- 0.2

100 PE

28.3 +/- 0.2 *

10

18

2

2.5, 0

32

100 PE

31.9 *

1

18

2

0, 0

0

0

0

Roche 454 GS FLX

1,500

0

2

0.30, 0.38

32.5 +/- 0.7

408 +/- 11

15.4 +/- 0.4

10

15 (LA)

3

0.91, 0.90, 0.85

32.8 +/- 0.8

377 +/- 15

31.5 +/- 4.0

0.01

25 (LA)

3

Ion Torrent PGM 316 chip

1,000

5

2

2.3, 2.4

16.3 +/- 0.2

105 +/- 5

40.3 +/- 7.6

ABI 3730xl

8,000

0

1

0.7

44.6

603

7.9

Experiment 2

Tara Oceans Station 41

Illumina HiSeq 2000

10

9 (N)

1

20.3

34.8

101 PE

36.3

10

12

2

18.6, 31.3

34.2 +/- 0.2

101 PE

36.2 +/- 0.9

10

15

1

15.4

34.3

101 PE

35.7

100

12

1

17.7

34.6

101 PE

35.0

Tara Oceans Station 109

Illumina HiSeq 2000

10

9 (N)

1

2.6

34.9

101 PE

35.4

10

12

1

20.4

34.9

101 PE

34.3

10

15

2

28.6, 16.2

34.4 +/- 0.5

101 PE

33.6 +/- 0.6

100

12

1

16.7

34.8

101 PE

34.3

  1. Starting DNA refers to the amount of pre-size selection DNA used in library construction; Library amplification abbreviations are LA = linker amplification and N = Nextera; Raw quality scores reported are PHRED scores; Raw length ‘PE’ denotes paired end reads. * denotes the successful 10ng library and one of the 100 ng libraries had an additional 40% of QC-passed reads that were lost due to removal of TruSeq adaptor sequence contaminants.