| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Critical commercial assays | ||
| CleanPlex SARS-CoV-2 Research and Surveillance panel | Paragon Genomics | Cat#918002 |
| CleanPlex for MGI Single-Indexed PCR Primers | Paragon Genomics | Cat#318007 |
| CleanMag Magnetic Beads | Paragon Genomics | Cat# 718003 |
| MGIEasy circularization kit | MGI | Cat#1000005259 |
| DNBSEQ-G50RS High-throughput Sequencing Set | MGI | Cat# 1000019859 |
| Qubit RNA HS assay kit | Invitrogen | Cat# Q32852 |
| Deposited data | ||
| NCBI BioProject ID PRJNA863945 | This paper | https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA863945 |
| Software and algorithms | ||
| SARS-CoV-2_Multi-PCR_V1.0 pipeline | MGI Tech bioinformatics | https://github.com/MGI-tech-bioinformatics/SARS-CoV-2_Multi-PCR_v1.0 |
| SOAPnuke filtration toolkit (version 2.0.6) | Chen at al 201847 | https://github.com/BGI-flexlab/SOAPnuke |
| BWA (version 0.7.17) | Li 201356 | https://github.com/lh3/bwa |
| Samtools (version 1.7) | Danecek et al. 202150 | https://github.com/samtools/samtools |
| Fgbio software package | https://github.com/fulcrumgenomics/fgbio | |
| LoFreq (version 2) | Wilm et al. 201255 | https://csb5.github.io/lofreq/ |
| GraphPad Prism 9.0 | www.graphpad.com | |
| R (version 4.2.1) | www.R-project.org | |
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