Table 2 Illumina DNA sequencing metrics, before and after preprocessing.

Library Type	Insert Size (bp)	Illumina Sequencer	Read Length	Number libraries	Original Number of Reads	Reads Kept After Pre-processing	Percentage reads kept
Paired-End	170	HiSeq 2000	100	3	983,306,498	833,615,836	84.8
	300	HiSeq X Ten	150	6	5,648,976,124	4,637,949,574	82.1
	500	HiSeq 2000	100	3	924,063,928	750,835,264	81.3
	800	HiSeq 2000	100	3	622,761,676	467,933,516	75.1
Mate-Pair	2000	HiSeq 2000	49	6	1,419,111,502	1,166,743,086	82.2
	5000	HiSeq 2000	49	3	501,967,462	404,751,694	80.6
	10000	HiSeq 4000	49	3	202,568,340	124,339,922	61.4
	20000	HiSeq 4000	49	3	258,232,918	157,943,444	61.2

When necessary, the reads were trimmed, using Sickle’s sliding window approach, to a minimum length of 120, 80 and 40 nucleotides, for the PE150, PE100 and MP libraries, respectively. The minimum quality over the set window size for each library type was 20.

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