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

The described data processing and read classification steps were implemented using the Snakemake workflow management system 53 and are available on Github -together with all necessary downstream analysis scripts to reproduce the results of this manuscript (https://github.com/d-j-k/puntseq). We gathered read statistics such as quality scores and read lengths using NanoStat (version 1.1.2, https://github.com/wdecoster/nanostat), and used Pistis (https://github.com/mbhall88/pistis) to create quality control plots. This allowed us to assess GC content and Phred quality score distributions, which appeared consistent across and within our reads. Overall, we obtained 2,080,266 reads for April, 737,164 for June, and 5,491,510 for August, with a mean read quality of 10.0 (Supplementary Table 2c ).