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Table 3 Mapping rates for different adapter clipping and read merging methods

From: EAGER: efficient ancient genome reconstruction

Sample Method Number of Mapped
   mapped reads reads [%]
3077 Clip&Merge 1,043,672 17.31
  MergeTrimReads 1,006,194 16.7
  CutAdapt + FLASH 1,036,940 17.2
  SeqPrep 949,073 15.74
  LeeHom 981,558 16.28
  AdapterRemoval 931,529 15.45
Jorgen625 Clip&Merge 2,703,428 17.9
  MergeTrimReads 2,623,243 17.37
  CutAdapt + FLASH 2,599,158 17.21
  SeqPrep 2,595,366 17.19
  LeeHom 2,617,909 17.34
  AdapterRemoval 2,524,087 16.71
Refshale16 Clip&Merge 13,368,593 33.49
  MergeTrimReads 13,812,705 34.6
  CutAdapt + FLASH 11,533,714 28.9
  SeqPrep 11,516,472 28.85
  LeeHom 8,916,759 22.34
  AdapterRemoval 11,431,717 28.64
SK2 Clip&Merge 48,536,318 89.48
  MergeTrimReads 48,610,983 89.62
  CutAdapt + FLASH 48,402,551 89.23
  SeqPrep 48,240,750 88.93
  LeeHom 48,337,919 89.11
  AdapterRemoval 47,095,207 86.82
SK8 Clip&Merge 1,283,126 12.96
  MergeTrimReads 1,280,119 12.93
  CutAdapt + FLASH 1,109,626 11.21
  SeqPrep 1,107,013 11.18
  LeeHom 908,549 9.18
  AdapterRemoval 1,100,326 11.12
LBK1 Clip&Merge 113,843,504 50.1
  CutAdapt + FLASH 52,681,090 26.8
  SeqPrep 109,491,426 51.6
  LeeHom 111,943,019 50.9
  AdapterRemoval 107,484,735 47.2
  1. Version 1.6 of Clip&Merge was tested. Version 1.7.1 of CutAdapt was evaluated together with version 1.2.11 of FLASH. We used SeqPrep version 1.1, and MergeTrimReads and LeeHom in the versions publicly available on 10 January 2015. Version 1.5.4 of AdapterRemoval was used. For the LBK1 sample, the MergeTrimReads method was not evaluated, as the run time of the method had exceeded those of all other methods when tested on smaller data sets by far. Overall, the tools Clip&Merge and MergeTrimReads performed best