Vcorn SARS-CoV-2
		Database of viral gene mutation

• Updated at 2022-03-12.

 ★ Pipeline

  ♦ Folder preparation

• “blast”, in which BLAST analysis is executed, is vacant at default setting.
• “db” contains database files for BLAST analysis (click here to download them).
• “info” contains files of sample information (click here to download them).
• “mut” contains a file on WHO-labelled variants (click here to download it).
• “net” contains files on networks between mutations (click here to download them).
• “org”, in which files downloaded from the NCBI Virus SARS-CoV-2 Data Hub are restored, is vacant at default setting.
• “perl” contains Perl scripts (click here to download them).
• “teto”, in which intermediate files on WHO-labelled variants are saved, is vacant at default setting.

  ♦ Download

• Mutation list, “mutations.csv”, is obtained from the NCBI Virus SARS-CoV-2 Data Hub, and is renamed to “mutations20220302.csv”.
• A file of the metadata of genome samples with version, “sequences.csv”, containing the columns of Accession, Release_Date, Length, Nuc_Completeness, Geo_Location, and Collection_Date, is obtained from the same website, and is renamed to “sequences20220302.csv”.
• A file of genome sequences adding the “BioSampl” ecolumn, “sequences.fasta”, is obtained from the same website, and is renamed to "sequences20220302.fasta."

  ♦ Pre-blast treatment

• “chknat.pl” & “mkpidsummary.pl” create files that contains meta data of the SARS-CoV-2 samples.

  ♦ BLASTN execution

• A BLASTN program is executed using the following command in the “blast” folder.
• “blastn -query ../org/sequences20220302.fasta -db ../db/modelS -out genome2modelSblastn.txt -outfmt "6 std btop"”

  ♦ Post-blast treatment

• “mkpid2mutS.pl” creates the file that relates samples to the base mutations harbored in the samples.

  ♦ Mutation analysis

• “mkmutS2member.pl” & “mkmutS2hgvs.pl” create files that relate base mutations to the samples & their amino acid codes.
• “count4mut2mut.pl” & “calprec4mut.pl” create files that relates each mutation to the other mutations.
• “outlier.pl”, “mkmuttable.pl”, “mkmut4timeseries.pl” & “mkmut4natdate.pl” create files that shows meta data of each mutation.

  ♦ Network analysis

• “mkmajormutsnet.pl”, “mdfnet.pl” & “resizenetsvg.pl” create network files that are used to depict relationships between the major mutations with the Pajek tool.
• “major2major.pl”, “calhi.pl” & “calshare4majormutpair.pl” create files that represent relationships between the major mutations.
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  ♦ Variant analysis

• The following Perl scripts create files that represent informtion on the WHO-labeled variants: “teto1net4var.pl”, “teto2ts.pl”, “teto3mdftrans.pl”, “teto4sel4who.pl”, “teto5selmuts4who.pl”, “teto6calrecall.pl”, “teto7mkrecallnet.pl”, “teto8del4delta.pl” & “teto9selmuts4who2.pl”.
• “mkpid2var.pl” & “mkvar2natdate.pl” create files that relate each variant to a nation & a date.

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