REAGENT or RESOURCE	SOURCE	IDENTIFIER
Critical commercial assays
Helix ® COVID-19 Test	Helix	EUA201636
TaqPath COVID-19 Combo Kit	Thermo Fisher	Cat#A47814
Illumina CovidSeq Test	Illumina	1000000128490 v01
MagMAX Viral/Pathogen II Nucleic Acid Isolation Kit	Thermo Fisher	Cat#A48383
Omega BioTek MagBind Viral DNA/RNA Kit	Omega Biotek	Cat#M6246-03
Nextera XT	Illumina	Cat#FC-131-1096
Illumina NextSeq with 500/550 Mid Output Kit v2.5	Illumina	Cat#20024908
Illumina NovaSeq 6000 with SP Reagent Kit v1.5	Illumina	Cat#20028400
Nanopore MinION KAPA HyperPrep kit	Roche	Cat#07962363001
End-repair and Ligation Sequencing Kit	Oxford Nanopore	Cat#SQK-LSK109
Quick-DNA/RNA Viral MagBead kit	Zymo Research	Cat#R2141
Illumina NovaSeq 6000 S4 flow cell & Reagent Kit v1.5	Illumina	Cat#20044417
Illumina NovaSeq Xp 4-lane Kit v1.5	Illumina	Cat#20042337
Omega BioTex MagBind Viral DNA/RNA Kit	Omega Biotek	Cat#M6246-03
KindFisher Flex Purification System	Thermo Fisher	Cat#5400630
Protoscript First Strand cDNA Synthesis Kit	NEB	Cat#E6560L
Q5 Hot Start High-Fidelity DNA Polymerase Kit	NEB	Cat #0493L
NEBNext Ultra II DNA Library Kit for Illumina	NEB	Cat#E7645L
MiSeq Reagent Kit V2	Illumina	Cat#MS-102-2002
Deposited data
SARS-CoV-2 reference genome	NCBI	NCBI: NC_045512.2
B.1.1.7 first identified sequence	GISAID	GISAID: EPI_ISL_601443
B.1.1.7 outgroup	NCBI	NCBI: NC_045512
BEAST XML and log files	This paper	https://github.com/andersen-lab/paper_2021_early-b117-usa
Non-US B.1.1.7 and additional B.1.1 lineage sequences	GISAID	Data S2
US B.1.1.7 sequences	This paper; GISAID	Data S2
SGTF and B117 ongoing Summary Level Data	This paper	Data S2; https://github.com/myhelix/helix-covid19db
Oligonucleotides
SARS-CoV-2 primers	Quick et al., 2017	N/A
NEBNext Multiplex Oligos for Illumina	NEB	Cat#E6440L
ARTIC Network n-CoV-19 V3 primers	ARTIC Network	https://github.com/artic-network/artic-ncov2019/tree/master/primer_schemes/nCoV-2019/V3
Software and algorithms
DRAGEN COVIDSeq Test Pipeline v.1.3.0.28	Illumina	N/A
Pangolin v2.0	O’Toole et al., 2021b	https://github.com/cov-lineages/pangolin
NextClade v0.12.0	Hadfield et al., 2018	https://github.com/nextstrain/nextclade
Iqtree2	Minh et al., 2020	https://github.com/iqtree/iqtree2
BEASTv1.10.5pre	Suchard et al., 2018	https://github.com/beast-dev/beast-mcmc/tree/v1.10.5pre_thorney_v0.1.0
BEAGLE	Ayres et al., 2019	https://faculty.washington.edu/browning/beagle/beagle.html#download
baltic		https://github.com/evogytis/baltic
Chiu lab genome assembly & variant calling	Deng et al., 2020	N/A
Andersen Lab consensus calling for nanopore data		https://github.com/artic-network/artic-ncov2019
Snakemake	Köster and Rahmann, 2012	https://snakemake.readthedocs.io/en/stable/
bwa-mem	Li, 2013	https://github.com/lh3/bwa
iVar v1.2.2	Grubaugh et al., 2019b	https://github.com/andersen-lab/ivar/releases/tag/v1.2.2
Transmissibility estimation	Volz et al., 2021	N/A
Conditional reference prior for overall clock rate	Ferreira and Suchard, 2008	N/A