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| -rw-r--r-- | README.md | 13 |
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@@ -8,6 +8,19 @@ Run the uploader with a FASTA file and accompanying metadata: python3 bh20sequploader/main.py example/sequence.fasta example/metadata.json +# Add a workflow + +get your SARS-CoV-2 sequences from GenBank in seqs.fa + +```sh +minimap2 -cx asm20 -X seqs.fa seqs.fa >seqs.paf +seqwish -s seqs.fa -p seqs.paf -g seqs.gfa +odgi build -g seqs.gfa -s -o seqs.odgi +odgi viz -i seqs.odgi -o seqs.png -x 4000 -y 500 -R -P 5 +``` + +from https://github.com/virtual-biohackathons/covid-19-bh20/wiki/Pangenome#pangenome-model-from-available-genomes + # Installation This tool requires the arvados Python module which can be installed |