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