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| author | Pjotr Prins | 2020-04-06 16:49:19 -0500 |
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| committer | Pjotr Prins | 2020-04-06 16:49:19 -0500 |
| commit | 762b770eda79fd4006b767e2dd768746232995ba (patch) | |
| tree | 6d6a69ef2ebf4a9481a2c350914373ad25f63d00 /README.md | |
| parent | e8eb3d7eba3fdaa925b45bd914bf6b5d65682d7f (diff) | |
| download | bh20-seq-resource-762b770eda79fd4006b767e2dd768746232995ba.tar.gz bh20-seq-resource-762b770eda79fd4006b767e2dd768746232995ba.tar.lz bh20-seq-resource-762b770eda79fd4006b767e2dd768746232995ba.zip | |
Add note on workflow
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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 |