Defining Paralogy Relationships among Haplotype Core Duplicons

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coredupgraph
coredupgraph
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Pipeline relating haplotype core duplicons to each other to define paralogy.

This is a Snakemake project template. The Snakefile is under workflow .

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    shell:'''
minimap2 -ax asm20 --secondary=yes -p 0.3 -N 10000 --eqx -r 500 -K 500M {input.hap_asm_fa} {input.locus_fa} | \
    samtools view -b - | samtools sort | \
    bedtools bamtobed -i - > {output.core_bed} || touch {output.core_bed}    
'''
SnakeMake SAMtools BEDTools Minimap2 From line 96 of workflow/Snakefile

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Created: 1yr ago
Updated: 1yr ago
Maitainers: public
URL: https://github.com/Xavster838/coreDupGraph
Name: coredupgraph
Version: 1
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Copyright: Public Domain
License: MIT License
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