REAGENT or RESOURCE	SOURCE	IDENTIFIER
Biological Samples
Plasma from COVID-19 patients (UCSF samples)	University of California, San Francisco	N/A
Plasma from patients with viral infections (excluding SARS-CoV-2)	University of California, San Francisco	N/A
Plasma from COVID-19 patients (MUHC samples)	McGill University Health Center	N/A
Plasma from healthy individuals	Cornell University	N/A
Critical Commercial Assays
QIAGEN MinElute Circulating Nucleic Acid Kit	QIAGEN	55204
QIAGEN EZ1 Virus Mini Kit v2.0	QIAGEN	955134
QIAGEN Circulating Nucleic Acid Kit	QIAGEN	55114
Zymo EZ Methylation-Gold kit (for bisulfite conversion)	Zymo	D5005
Swift Biosciences Accel-NGS Methyl-Seq DNA Library Kit	Swift	30024
Deposited Data
Genomic data	This manuscript	PRJNA687910 (NCBI Sequence Read Archive)
Methylation data	This manuscript	https://www.github.com/alexpcheng/cfDNAme
Oligonucleotides
cfDNA concentration control 5′- TTTAACGCATAAACATGCGTTT TGGGTAGTGTTTTTTGGAAACACAG ATCCGTGCGCACACCTGGTGGAG-3′	Integrated DNA Technologies	https://www.idtdna.com/pages
cfDNA concentration control 2 5′- ATAAACATGCGTTTTGGG TAGTGTTTTTTGGAAA CACAGATCCGTGCGCACACCT-3′	Integrated DNA Technologies	https://www.idtdna.com/pages
cfDNA concentration control 3 5′- GCGTTTTGGGTAGTGTTTTTT GGAAACACAGATCCGTGCG-3′	Integrated DNA Technologies	http://www.idtdna.com/pages
cfDNA concentration control 4 5′-GGTAGTGTTTTTTGG AAACACAGAT-3′	Integrated DNA Technologies	http://www.idtdna.com/pages
Software and Algorithms
Custom scripts	This manuscript	https://www.github.com/alexpcheng/cfDNAme
BBTools	52	https://jgi.doe.gov/data-and-tools/bbtools/
Bismark	53	https://github.com/FelixKrueger/Bismark
SAMtools	54	http://www.htslib.org/
Metilene	55	https://www.bioinf.uni-leipzig.de/Software/metilene/
MethPipe	56	https://github.com/smithlabcode/methpipe
Other
DELFI pipeline	41	https://github.com/Cancer-Genomics/delfi_scripts
Illumina NextSeq 500	Illumina	https://www.illumina.com
Illumina NovaSeq	Illumina	https://www.illumina.com