title: Raw reads: W36Y23Mal
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 Malmo, 2023-W36. 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.