REAGENT or RESOURCE	SOURCE	IDENTIFIER
Critical commercial assays
CleanPlex SARS-CoV-2 Flex Panel	Paragon Genomics, CA, USA	Cat.# 918015
Mid output NextSeq500	Illumina, CA, USA	Cat.# 20024905
CleanPlex plated Unique Dual-Indexed PCR Primers for Illumina Set C	Paragon Genomics, CA, USA	Cat.# 716037
CleanPlex plated Unique Dual-Indexed PCR Primers for Illumina Set D	Paragon Genomics, CA, USA	Cat.# 716038
CleanPlex plated Unique Dual-Indexed PCR Primers for Illumina Set E	Paragon Genomics, CA, USA	Cat.# 716039
CleanPlex plated Unique Dual-Indexed PCR Primers for Illumina Set F	Paragon Genomics, CA, USA	Cat.# 716040
cobas® SARS-CoV-2	Roche	Cat.# 09175431190
cobas® SARS-CoV-2 Control Kit	Roche	Cat.# 09175440190
cobas® 6800/8800 Buffer Negative Control Kit	Roche	Cat.# 07002238190
MagNA Pure 96 DNA and Viral Nucleic Acid Small Volume Kit	Roche	Cat.# 06543588001
Deposited data
All SARS-CoV2 sequences are available at	ENA	PRJEB50471
Software and algorithms
FastQC	Andrews S. (2010).	https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Cutadapt	Martin M. (2011).	https://cutadapt.readthedocs.io/en/stable/
Vsearch	Rognes T. (2016).	https://github.com/torognes/vsearch
FASTX-Toolkit	Hannon, G.J. (2010)	http://hannonlab.cshl.edu/fastx_toolkit/
Samtools	Danecek P. (2021).	https://github.com/samtools/samtools
Sambamba	Tarasov A. (2015).	https://lomereiter.github.io/sambamba/
Samclip	N/A	https://github.com/tseemann/samclip
bamaddrg	N/A	https://github.com/ekg/bamaddrg
seqtk	N/A	https://github.com/lh3/seqtk
iVAR	Grubaugh, N.D. (2019).	https://github.com/andersen-lab/ivar
bedtools	Aaron R. Quinlan (2010).	https://bedtools.readthedocs.io/en/latest/
Frrebayes	Garrison E. (2012).	https://github.com/freebayes/freebayes
bcftools	Danecek P. (2021).	https://samtools.github.io/bcftools/bcftools.html
vcflib	Garrison E.	https://github.com/vcflib/vcflib
Pangolin	O’Toole A. (2021).	https://github.com/stevenlovegrove/Pangolin
Nexstrain	Aksamentov, I. (2021).	https://clades.nextstrain.org/