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Table 6 Comparison of duplicate reads obtained for the same libraries sequenced on both HiSeq 2500 and HiSeq X Ten

From: Guidelines for whole genome bisulphite sequencing of intact and FFPET DNA on the Illumina HiSeq X Ten

Library preparation method Library preparation kit Input amount (ng) Sequencing platform DNA samples Raw reads Duplicate reads (%) Coverage Ratio of CpG islands/shores
Post-BS TruMethyl WG v1.9 200 HiSeq 2500 Rapid runa 1. Cell line (B80-T17-p12) 303298084 2.0 9.12× 1.0:1.1
2. Cell line (B80-T17-p95) 412412960 2.7 12.40× 0.9:1.1
3. Cell line (B80-T8-p8) 309366352 1.9 9.48× 1.0:1.1
4. Cell line (B80-T8-p46) 337623632 2.2 10.20× 1.0:1.1
5. Cell line (MCF7) 232184682 1.6 7.24× 1.0:1.1
6. Cell line (TAMR) 28866392 1.2 6.66× 1.0:1.1
HiSeq X Ten 1. Cell line (B80-T17-p12) 549,330,057 18 16.41× 1.0:1.1
2. Cell line (B80-T17-p95) 623,032,192 18 18.83× 0.8:1.0
3. Cell line (B80-T8-p8) 534,563,634 15 16.84× 1.0:1.1
4. Cell line (B80-T8-p46) 551,950,690 16 17.24× 1.0:1.1
5. Cell line (MCF7) 634,201,220 19 23.43× 0.9:1.0
6. Cell line (TAMR) 571,714,843 15 20.48× 0.9:1.0
  1. aOne rapid run is two lanes