Journal: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
Article Title: Comparison of the sequencing bias of currently available library preparation kits for Illumina sequencing of bacterial genomes and metagenomes
Figure Lengend Snippet: Quality comparison of E. coli and S. aureus genome assemblies obtained by library preparation kits. (A) Assembly statistics obtained by six library preparation kits were compared in E. coli and S. aureus . Two E. coli and two S. aureus genomes were analysed as model bacterial genomes to compare six library preparation kits. Illumina read sequences obtained from each library were assembled using Velvet and SPAdes, and the numbers of contigs and L50 values of each assembly are shown. In each sequence data set, assembly was repeated 10 times using Illumina reads randomly selected at 30× coverage. Error bars indicate standard deviations. The six kits used cover three fragmentation strategies (see the main text). XT, Nextera XT; FL, Nextera DNA Flex; KP, KAPA HyperPlus; NN, NEBNext Ultra II; QS, QIAseq FX; and TS, TruSeq nano. (B) Relative sequence coverage in relation to GC content was calculated in E. coli and S. aureus genomes obtained by three library preparation kits. Relative sequence coverage in the genome assemblies obtained by the XT, FL, and KP kits and GC content were calculated for every 200-bp window with no overlap. Only the first 120,000 bp regions of each genome are shown. (C) Relationships between GC content and sequence coverage in the E. coli and S. aureus genome assemblies obtained by six library preparation kits are shown. The relative abundance of 200 bp bins with a given GC content (defined by 0.5% interval) and the mean relative coverage of bins with a given GC content ( C GC ) were calculated and are shown along with GC content by black lines or lines coloured according to the library preparation kits, respectively. Black horizontal lines ( C GC =1) represent unbiased coverage. The data for bins with extreme GC content (those representing
Article Snippet: Library preparation and sequencing Eight sequencing library preparation kits were used in this study: XT, KAPA HyperPlus (NIPPON Genetics Co. Ltd, Tokyo, Japan) with PCR or PCR-free workflow (referred to as KP and KPF, respectively), NEBNext Ultra II (referred to as NN; New England Biolabs Japan, Tokyo, Japan), QIAseq FX (QS; QIAGEN), TruSeq nano (TS; Illumina), TruSeq DNA PCR-Free (TSF; Illumina), and Nextera DNA Flex (FL; Illumina) ( ).