Raw fastq reads were adapter trimmed using Cutadapt v 1.1245, followed by quality trimming and quality filtering using the FASTX Toolkit (Hannon Lab, CSHL). Reads were paired up and aligned to the SARS-CoV-2 genome from isolate SARS-CoV-2/humanUSA/WA-CDC-WA1/2020 (MN985325.1) using Bowtie2 v 2.2.946. PCR duplicates were removed using Picard MarkDuplicates v 2.18.7 (Broad Institute). Variant detection was performed using GATK HaplotypeCaller v with ploidy set to 2.

Note: The content above has been extracted from a research article, so it may not display correctly.

Please log in to submit your questions online.
Your question will be posted on the Bio-101 website. We will send your questions to the authors of this protocol and Bio-protocol community members who are experienced with this method. you will be informed using the email address associated with your Bio-protocol account.

We use cookies on this site to enhance your user experience. By using our website, you are agreeing to allow the storage of cookies on your computer.