Optimized Illumina PCR-free library preparation for bacterial whole genome sequencing and analysis of factors influencing de novo assembly

Table 2 Sequencing library categories

Library category	Fragmentation parameters	RB:BB ratios	Avg. insert size (raw data) (bps)	Sequenced genomes
TS	DF 5 %, PIP 175 W, C/B 200, Du 25 s	TruSeq^® DNA PCR-free LPP (LS protocol, 550 bps)	641 ± 28	Bce, Efa, Pst, Mlu
IS1	DF 10 %, PIP 175 W, C/B 200, Du 25 s	2.0:1 + 3.8:2	686 ± 33	Bce, Efa, Sen, Pst, Mlu
IS2	DF 2 %, PIP 175 W, C/B 200, Du 30 s	2.2:1 + 4.2:2	990 ± 79	Efa, Sen, Mlu₅₀
IS3	DF 2 %, PIP 175 W, C/B 200, Du 20 s	2.3:1 + 4.4:2	1211 ± 78	Bce, Pst, Mlu, Mlu₅₀
IS4	DF 2 %, PIP 175 W, C/B 200, Du 10 s	2.4:1 + 4.6:2	1297	Mlu₅₀

Settings for genomic DNA fragmentation and fragment size selection during library preparation. TS, original Illumina TruSeq^® DNA PCR-free LLP (no modification)
IS1-IS4, categories for library average insert size, where IS1 < IS2 < IS3 < IS4
The term Mlu₅₀ refers to the corresponding genome sequenced at 2 × 25 bps. Genomes listed without index were sequenced at 2 × 200 bps throughout
Bce B. cereus, Efa E. faecalis, Pst P. stutzeri, Mlu M. luteu, Sen S. enterica, RB Resuspension Buffer, BB Bead Buffer, DF Duty Factor, PIP Peak Incident Power, C/B Cycles per Burst, Du Duration

ISSN: 1756-0500