This has the analyses for Peacock, Goldhill, Zhou, Baillon and Frise et al. 2021 Nature Microbiology. Available in an earlier form on bioRxiv at https://www.biorxiv.org/content/10.1101/2020.09.30.318311v1
For the barcoded NGS sequencing, the sequences can be downloaded from ebi.ac.uk/ena, project PRJEB40394, samples DG-Pool-1 to DG-Pool-24. (Each pool contains 2 or 3 samples with an internal barcode as described on the spreadsheet NGS Sample Sheet Clean.) Download the sequences and put them in their own folder.
For the post-mortem sequencing...
To find the spike deletions- I downloaded a total of 100,690 SARS-CoV-2 genomes from GISAID (www.gisaid.org) on 16/9/2020 and aligned them to 234bp from the spike protein using Geneious. I trimmed the alignment to the length of the reference sequence and this gave the file subseqs_09-16-20.fasta which is available as a zipped file in this repository. Download and unzip subseqs_09-16-20.fasta.zip and run FindSARSCoV2Dels(). It produces samples of interest which must then be reexamined on GISAID to ensure they are human samples which have not been passaged.