merqury_trio_scaffolds.pbs

#!/bin/bash
#PBS -q condo05
#PBS -l select=1:ncpus=64:mem=502GB
#PBS -l walltime=168:00:00
#PBS -W group_list=x-ccast-prj-hulke
#PBS -N funTimesWithMerqury

# Load modules
module load samtools/1.20
module load r/4.4.0
module load bedtools/2.30.0

# Set directory
cd /mmfs1/projects/brent.hulke/MutagenesisSmart/HudsonAlpha/HifiParentalIlluminaOmniCAssembly/merqury_trio/merqury_scaffolds

export MERQURY=/mmfs1/projects/brent.hulke/Software/merqury
export PATH="/mmfs1/projects/brent.hulke/Software/meryl-1.4.1/bin:$PATH"

$MERQURY/merqury.sh /mmfs1/projects/brent.hulke/MutagenesisSmart/HudsonAlpha/hifi_kmers_k21.meryl \
    ../HomoGreen.meryl \
    ../HomoRed.meryl \
    /mmfs1/projects/brent.hulke/MutagenesisSmart/HudsonAlpha/HifiParentalIlluminaOmniCAssembly/yahs_scaffolding_trio_hap1/yahs.out_scaffolds_final_hap1.fa \
    /mmfs1/projects/brent.hulke/MutagenesisSmart/HudsonAlpha/HifiParentalIlluminaOmniCAssembly/yahs_scaffolding_trio_hap2/yahs.out_scaffolds_final_hap2.fa \
    TrioMerquryScaffolds