Wastewater in-silico NGS dataset

This dataset comprises 45 paired-end wastewater next-generation sequencing (NGS) samples generated in-silico using the SWAMPY tool (https://doi.org/10.1093/bioinformatics/btae532). In particular, we produced 500000 reads per sample (--n_reads 500000) to simulate MySeq runs (--seqSys MSv3) with the ARTIC amplicon panel v.4 (--primer_set a4).
Each sample includes three different SARS-CoV-2 lineages (JN.1-Omicron: EPI_ISL_18850060, AY.99.2-Delta: OM898676, BA.2-Omicron: OV754178) in varying proportions. Overall, there are five different datasets. Within each dataset (consisting of nine samples), the frequency of JN.1 is kept fixed while the relative abundance of the other two lineages varies inversely. The fixed frequencies of JN.1 are 0%, 5%, 10%, 30%, and 50%.

- When JN.1 is at 50%, AY.2 ranges from 5% to 45% while BA.2 decreases from 45% to 5%.

- When JN.1 is at 30%, AY.2 ranges from 7% to 63% while BA.2 decreases from 63% to 7%.

- When JN.1 is at 10%, AY.2 ranges from 9% to 81% while BA.2 decreases from 81% to 9%.

- When JN.1 is at 5%, AY.2 ranges from 10% to 90% while BA.2 decreases from 85% to 5%.

- When JN.1 is at 0%, AY.2 ranges from 10% to 90% while BA.2 decreases from 90% to 10%.

Filenames are encoded with the following information: Presence/Absence of JN.1; Frequency of JN.1; AY.99.2 ID; AY.99.2 Frequency; BA.2 ID; BA.2 Frequency; Instrument Model; Nreads (e.g., Positive.JN1.5.OM898676.80.OV754178.15.MSv3.WW.500000reads_R1.fastq.gz)