linear pangenome for crops

Question

[analyst]

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

[Sony]

This is an example pipeline for constructing linear pangenome for beans using NGS seq data, https://www.researchgate.net/publication/338329301_Legume_Pangenome_Construction_Using_an_Iterative_Mapping_and_Assembly_Approach

Answer 1

[Semir]

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