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
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.
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