REAGENT or RESOURCE	SOURCE	IDENTIFIER
Critical commercial assays
COVIDSeq Assay (96 samples)	Illumina	Cat# 20049393
COVIDSeq v4 Primer Pools	Illumina	Cat# 20065135
Quick-RNA Viral 96 Kit	Zymo Research	Cat# R1041
MagMAX™ Viral/Pathogen II (MVP II) Nucleic Isolation Kit	ThermoFisher	Cat# A48383
Applied Biosystems TaqPath Master Mix no ROX	ThermoFisher	Cat# A28523
CDC 2019-nCoV Real-Time RT-PCR Primers and Probes	IDT	Custom; see (Landaverde et al., 2022)
Deposited data
Raw sequencing data	NCBI Bioproject	Bioproject: PRJNA867488
Community consensus sequences	GISAID EPI_SET	EPI_SET: EPI_SET_220804bm
Software and algorithms
Bowtie2	bowtie-bio.sourceforge.net	v2.3.4.1
Samtools	htslib.org	v1.15.1
LoFreq	csb5.github.io/lofreq	v2.1.3.1
R	r-project.org	v4.0.2
Pangolin	pangolin.cog-uk.io	v4.1.1
Pango data	pangolin.cog-uk.io	v1.11
tidyverse	tidyverse.org	v1.3.0
argparse	github.com/trevorld/r-argparse	v2.1.5
BEAST	github.com/beast-dev/beast-mcmc	v1.10.4