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linear pangenome for crops

Dear all,

Can you please guide how can I construct linear pangenome for a plant that can be used as a reference genome for variant calling of my plant reads later on?

Thanks a lot

pangenome linear
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updated by Sony Nguyen • Sony Nguyen • written by Bushra Bibi Bushra Bibi

1 answer

You can use Cactus to do so:

cactus-align ./jobstore \
    seqFile.txt \
    alignment.maf \
    --reference ${reference_genome} \
    --maxCores ${task.cpus} \
    --maxMemory ${task.memory.toGiga()}

I generated this answer using amplicon.ai, a tool I've been building to iteratively write and execute bioinformatics code easier. Feel free to try it out

enter image description here

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written by Semir • Semir

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