gisaid_cov2020_sequences_0407.zip all sequences used
align_mutation_calling.sh is the shell script use to alignment and calling mutations for each SARS-CoV-2 sequences
mutation_analysis.R the Rscript to analysis the mutations
the_mutations_with_annotation.vcf is the mutations with annotation of the SARS-CoV-2 sequences
The graph genome of SARS-CoV-2 which is createed by vg
SARS-CoV-2.vg is the graph genome file constructed by vg
The index files are also included.
SARS-CoV-2.xg is the xg index of graph genome SARS-CoV-2.vg
SARS-CoV-2.gcsa is the gcsa index of graph genome SARS-CoV-2.vg
SARS-CoV-2.gcsa.lcp is the linked file of SARS-CoV-2.gcsa
SARS-CoV-2.gfa is the gfa view of graph genome SARS-CoV-2.vg
SARS-CoV-2.svg is the svg view of graph genome SARS-CoV-2.vg