Table 3.

Mapping rates for different adapter clipping and read merging methods

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

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