Comparisons of library preparation methods
The feasibility of shallow shotgun sequencing depends on cost-effective library preparation methods. We observed minor differences between datasets created using Nextera XT and iGenomx Riptide preparations. These differences may derive from random variation introduced during laboratory processing, or might be artefacts of the deeper initial sequencing depth of the Nextera XT versus iGenomx Riptide prepared samples (30 versus 4.1 million read-pairs). Additionally, the 16-sample Nextera XT prepared library was sequenced alone on an Illumina Nextseq 500 platform, while the 188-sample iGenomx Riptide library was sequenced on an Illumina NovaSeq6000. More extensive multiplexing during sequencing of the iGenomx Riptide library may have resulted in greater index hopping-based cross-contamination between samples. Nonetheless, iGenomx Riptide library preparations do not appear to quantitatively bias shotgun metagenomic results. We conclude that iGenomx Riptide preparations enables accurate cost-efficient library preparation for high-throughput shallow shotgun sequencing. However, we note recent benchmarking suggests it might be unsuitable for degraded DNA samples