Freshwater monitoring by nanopore sequencing

Lara Urban; Andre Holzer; J Jotautas Baronas; Michael Hall; Philipp Braeuninger-Weimer; Michael J Scherm; Daniel J Kunz; Surangi N Perera; Daniel E Martin-Herranz; Edward T Tipper; Susannah J Salter; Maximilian R Stammnitz

This study was designed to enable freshwater microbiome monitoring in budget-constrained research environments. Although we had access to basic infrastructure such as pipettes, a PCR and TissueLyser II machine, as well a high-performance laptop, we wish to highlight that the total sequencing consumable costs were held below £4,000 (Supplementary Table 6a ). Here, individual costs ranged at ~£75 per sample (Supplementary Table 6b ). With the current MinION flow cell price of £720, we estimate that per-sample costs could be further reduced to as low as ~£15 when barcoding and pooling ~£100 samples in the same sequencing run (Supplementary Table 6c ). Assuming near-equimolar amplicon pooling, flow cells with an output of ~5,000,000 reads can yield well over 37,000 sequences per sample and thereby surpass this conservative threshold applied here for comparative river microbiota analyses.