Journal: Frontiers in Microbiology

Article Title: The efficiency of Nextera XT tagmentation depends on G and C bases in the binding motif leading to uneven coverage in bacterial species with low and neutral GC-content

doi: 10.3389/fmicb.2022.944770

Figure Lengend Snippet: Dependency on the total amount of data used for quality parameters in the Campylobacter jejuni PT 28 dataset. The data have been colored to indicate the type of library prep kit used (Nextera XT red, Nextera Flex/DNA Prep blue). (A) The number of contigs generated by SPAdes assembler after filtering short and low coverage contigs. (B) N50 values of the assemblies. (C) The percentage of the k -mers present in the completed reference sequence found in the assemblies. (D) Number of genes found by the annotation tool Prokka. (E) Number of cgMLST genes (Oxford schema) called by Ridom SeqSphere+. (F) Number of SNPs called by Snippy against the reference genome NC002163.1.

Article Snippet: In 2017, a new version of Nextera called Nextera DNA Flex was released.

Techniques: Generated, Sequencing

Journal: Frontiers in Microbiology

Article Title: The efficiency of Nextera XT tagmentation depends on G and C bases in the binding motif leading to uneven coverage in bacterial species with low and neutral GC-content

doi: 10.3389/fmicb.2022.944770

Figure Lengend Snippet: t -tests comparing Nextera XT labs with Nextera Flex/DNA Prep labs for the quality control data from Figure 1 at coverages 25X and 50X.

Article Snippet: In 2017, a new version of Nextera called Nextera DNA Flex was released.

Techniques: Control

Journal: Frontiers in Microbiology

Article Title: The efficiency of Nextera XT tagmentation depends on G and C bases in the binding motif leading to uneven coverage in bacterial species with low and neutral GC-content

doi: 10.3389/fmicb.2022.944770

Figure Lengend Snippet: Coverage fluctuations along the first 250 kb of the reference genome for the laboratories in the Campylobacter jejuni PT 28 dataset. The data have been downsampled to equal depth and colored to indicate the type of library prep kit used (Nextera XT red, Nextera Flex/DNA Prep blue). MAD refer to Mean absolute deviation.

Article Snippet: In 2017, a new version of Nextera called Nextera DNA Flex was released.

Techniques:

Journal: Frontiers in Microbiology

Article Title: The efficiency of Nextera XT tagmentation depends on G and C bases in the binding motif leading to uneven coverage in bacterial species with low and neutral GC-content

doi: 10.3389/fmicb.2022.944770

Figure Lengend Snippet: Connection between GC-content and coverage bias for the Campylobacter jejuni PT 28 dataset. The data have been colored to indicate the type of library prep kit used (Nextera XT red, Nextera Flex/DNA Prep blue). (A) Pearson’s correlation coefficients calculated between the sliding window coverage data and GC-content data. (B) Histogram over the GC-contents of the sequence reads. (C) Histogram over the depth of the reference sequence k -mers in the raw data downsampled to 50X (upper part) and the corresponding average GC-content of the k -mers in each histogram bin.

Article Snippet: In 2017, a new version of Nextera called Nextera DNA Flex was released.

Techniques: Sequencing

Journal: Frontiers in Microbiology

Article Title: The efficiency of Nextera XT tagmentation depends on G and C bases in the binding motif leading to uneven coverage in bacterial species with low and neutral GC-content

doi: 10.3389/fmicb.2022.944770

Figure Lengend Snippet: Base composition of Nextera tagmentation sites. (A) Average base composition of tagmentation sites relative to the read start position for the Nextera XT and Nextera Flex/DNA Prep data in the Campylobacter jejuni PT 28 dataset. (B) DNA Logo plot of the data shown in A. Both probability and bits indicating the importance of individual positions are plotted. (C) GC-content of the tagmentation sites when divided into groups of different cleavage efficiencies (higher usage frequency corresponds to higher cleavage efficiency). Note that the Nextera XT dataset had higher total coverage than the Nextera Flex/DNA Prep and therefore, the bins are set higher for that dataset. “LC regions” correspond to the tagmentation sites found in regions yielding low coverage when sequenced using Nextera XT, but the same regions were also analyzed in the Nextera Flex/DNA prep dataset.

Article Snippet: In 2017, a new version of Nextera called Nextera DNA Flex was released.

Techniques:

Journal: Frontiers in Microbiology

Article Title: The efficiency of Nextera XT tagmentation depends on G and C bases in the binding motif leading to uneven coverage in bacterial species with low and neutral GC-content

doi: 10.3389/fmicb.2022.944770

Figure Lengend Snippet: Coverage bias, connection to GC-content, and consequences on assembly efficiency for data produced with Nextera XT and Nextera Flex/DNA Prep in external datasets. The data have been colored to indicate the type of library prep kit used (Nextera XT orange/red, Nextera Flex/DNA Prep light blue/dark blue). Left column represents histograms over the depth in the raw data (downsampled to 50x) of the k -mers present in the reference sequence. Middle column represents the corresponding average GC-content of the k -mers in each histogram bin. The right column represents the number of contigs generated by SPAdes assembler after filtering short and low coverage contigs. (A) EURL- Campylobacter PT 28 data including Campylobacter jejuni and C. coli . (B–D) Data from an interlaboratory comparison made by BfR, Germany . Two strains each, of C. jejuni , L. monocytogenes, and Salmonella enterica . (E,F) Data from a study by . Two strains each, of Escherichia coli and Staphylococcus aureus .

Article Snippet: In 2017, a new version of Nextera called Nextera DNA Flex was released.

Techniques: Produced, Sequencing, Generated, Comparison

Journal: Frontiers in Microbiology

Article Title: The efficiency of Nextera XT tagmentation depends on G and C bases in the binding motif leading to uneven coverage in bacterial species with low and neutral GC-content

doi: 10.3389/fmicb.2022.944770

Figure Lengend Snippet: Coverage bias, connection to GC-content, and consequences on assembly efficiency for data produced with Nextera XT and Nextera Flex/DNA Prep in external datasets. The data have been colored to indicate the type of library prep kit used (Nextera XT red, Nextera Flex/DNA Prep blue). Left column represents histograms over the depth in the raw data (downsampled to 50x) of the k -mers present in the reference sequence. Middle column represents the corresponding average GC-content of the k -mers in each histogram bin. The right column represents the number of contigs generated by SPAdes assembler after filtering short and low coverage contigs. (A–F) Data from representing bacterial species with low GC-content.

Article Snippet: In 2017, a new version of Nextera called Nextera DNA Flex was released.

Techniques: Produced, Sequencing, Generated

Journal: Frontiers in Microbiology

Article Title: The efficiency of Nextera XT tagmentation depends on G and C bases in the binding motif leading to uneven coverage in bacterial species with low and neutral GC-content

doi: 10.3389/fmicb.2022.944770

Figure Lengend Snippet: Coverage bias, connection to GC-content, and consequences on assembly efficiency for data produced with Nextera XT and Nextera Flex/DNA Prep in external datasets. The data have been colored to indicate the type of library prep kit used (Nextera XT red, Nextera Flex/DNA Prep blue). Left column represents histograms over the depth in the raw data (downsampled to 50x) of the k -mers present in the reference sequence. Middle column represents the corresponding average GC-content of the k -mers in each histogram bin. The right column represents the number of contigs generated by SPAdes assembler after filtering short and low coverage contigs. (A–F) Data from representing bacterial species with medium or high GC-content.

Article Snippet: In 2017, a new version of Nextera called Nextera DNA Flex was released.

Techniques: Produced, Sequencing, Generated