Fig 1.
Differences in uniformity of coverage between the Nextera XT and the DNA Prep kits.
(A, C, E) Coverage count data from three representative samples displayed as frequency histograms where mean coverage was very similar between the two kits (A), mean coverage was higher in the DNA Prep kit than the Nextera XT kit (C) and mean coverage was higher in the Nextera XT kit than the DNA Prep kit (E). (B, D, F) Coverage count data displayed as bar plots from three representative samples where the DNA Prep dataset showed more uniform coverage than the Nextera XT dataset despite mean coverage being comparable between the two kits (B), which was also the case where mean coverage was higher in the DNA Prep kit than the Nextera XT kit (D) and where mean coverage was higher in the Nextera XT kit than the DNA Prep kit (F).
Fig 2.
The relationship between GC-content and low coverage regions of the E. coli chromosome.
(A-C) Graph displays the GC-content percentage of low coverage regions (coverage less than 5, each region of length greater than 10 bp) of each representative E. coli sample.
Fig 3.
Comparison of mean sequencing coverage and number of reads per sample between the DNA Prep and Nextera XT kits.
(A) Difference in mean sequencing coverage between the Nextera XT and DNA Prep kits, (B) Variation in the number of reads per sample between the Nextera XT and DNA Prep kits.
Fig 4.
Comparison of average fragment size between the Nextera XT and DNA Prep kits.
The DNA Prep kit yielded fragments with a smaller and more tightly distributed size range compared to the Nextera XT kit.
Fig 5.
Tagmentation bias observed in both the Nextera XT and DNA Prep library preparation kits.
(A, B) The average proportion of each of the four bases at the first nine positions of each read is displayed here (A: Nextera XT, B: DNA Prep), indicating that a highly similar sequence motif is preferentially tagmented by the transposome in both library preparation kits (5’-GTNYWRNAC).
Fig 6.
Comparison of de novo assembly quality between the two library preparation kits.
(A-D) The difference in number of contigs per assembly (A), size of the largest contig in the assembly (B), total assembly length (C) and N50 based on which kit was used for library preparation.