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 |