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Three steps, and all you need is a terminal.

1. Install karyon

cargo install --git https://github.com/PathoGenOmics-Lab/karyon

cargo comes with Rust. If you do not have it, the one command at rustup.rs installs it.

2. Get the example files

Reads, variant calls, genes and the files of every other page, about 40 kilobytes in all:

curl -O https://pathogenomics-lab.github.io/karyon/data/examples.zip
unzip examples.zip

3. Draw them

karyon rpoB reads.bam genes.gff3 calls.vcf.gz -o rpoB.svg

The depth of the reads over the gene rpoB, with a stretch no read covers, the gene as an arrow, and seven variant calls as lollipops as tall as their allele frequency The same figure on the dark page

Open rpoB.svg in a web browser. Point at a call or a gene, and the browser says what it is and where.

How to read a command

  1. The place comes first: a gene, a sequence, or a region such as NC_000962.3:761,000-763,000.
  2. Then your files. Each one is a row, top to bottom in the order you write them.
  3. Then -o and the file to write.

Options for one row go right after its file: reads.bam --height 100.

Next

What do you have? has a page for each kind of data, with the command and the figure it draws.