title: Ion Torrent S5 XL sequencing; Aligned reads: 2022-W6 Kalmar Ion Torrent S5 XL wastewater sequencing using Ion AmpliSeq SARS-CoV-2 Insight Research Assay to report on circulating SARS-CoV-2 mutations
design: Ion Torrent S5 XL wastewater sequencing using Ion AmpliSeq SARS-CoV-2 Insight Research Assay to report on circulating SARS-CoV-2 mutations in Kalmar, 2022-W6.
library_construction_protocol: Viral genomic material was concentrated and extracted by the direct capture method using the Maxwell RSC Enviro Total Nucleic Acid Kit (Promega Corporation, Madison, WI, USA, Cat # AS1831) according to the manufacturer's protocol (Promega, # TM663 Rev 4/22) at SEEC-SLU. Sequencing libraries were made using Ion AmpliSeq SARS-CoV-2 Insight Research Assay (Thermo Fisher Scientific, Waltham, MA, USA, Cat # A51306) and the SuperScript™ VILO™ cDNA Synthesis Kit (Thermo Fisher, # 11754050) according to the manufacturer's protocols “Reverse transcribe RNA with the SuperScript™ VILO™ cDNA Synthesis Kit” (Thermo Fisher, # MAN0019277, Rev B.0, pp. 3–4) and “Prepare libraries on the Ion Chef™ Instrument” (Thermo Fisher, # MAN0024915 Rev B.0, Ch 4, pp. 42–43) at the National Genomic Infrastructure (NGI) at SciLifeLab in Uppsala, Sweden. Sequencing was performed on the Ion S5 XL System (Thermo Fisher, # A27214) multiplexing using Torrent Suite Software version 5.16.1 configured according to the manufacturer's protocol (Thermo Fisher, # MAN0024915 Rev B.0, Ch2, Ch 5 and Ch 7) at NGI. The data generated from sequencing were filtered, demultiplexed and aligned to the manufacturers references (Ion_AmpliSeq_SARS-CoV-2-Insight_Reference) using the manufacturers analysis pipeline in Torrent Suite 5.16 (Thermo Fisher, # MAN0017972 Rev B.0, Ch 12) at NGI. The resulting files conformed to the conventions of Ion Torrent BAM format and were delivered with corresponding index files and a run report.