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add direct nucmer and mashmap subcommands to alignplot #165

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add direct nucmer and mashmap subcommands to alignplot #165

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@ctb ctb commented Dec 8, 2020

Usage:

run and plot a nucmer comparison

python -m charcoal.alignplot nucmer ibd-genomes-2/ZeeviD_2015__PNP_Main_232__bin.27.fa.gz genbank_genomes/GCF_003481565.1_genomic.fna.gz -o xyz

run and plot a mashmap comparison

python -m charcoal.alignplot mashmap ibd-genomes-2/ZeeviD_2015__PNP_Main_232__bin.27.fa.gz genbank_genomes/GCF_003481565.1_genomic.fna.gz -o xyz

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