Data associated the the manuscript "Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection"
| Filename | Description |
|---|---|
| SARS_CoV_2_Amplicon_processing_fragmented.bash | Script for mapping reads from amplicon-based sequencing to a reference genome and trimming primers |
| variant_calls.sh | Script for calling and annotating variants using the generated mapping files |
| combine_vcf.sh | Script for merging annotated variants |
Chrispin Chaguza, Anne M. Hahn, Mary E. Petrone, Shuntai Zhou, David Ferguson, Mallery I. Breban, Kien Pham, Mario A. Peña-Hernández, Christopher Castaldi, Verity Hill, Yale SARS-CoV-2 Genomic Surveillance Initiative, View ORCID ProfileWade Schulz, Ronald I. Swanstrom, Scott C. Roberts, Nathan D. Grubaugh. Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection. medRxiv. https://www.medrxiv.org/content/10.1101/2022.06.29.22276868v1 (under review).