minimap2assemblies.pbs

#!/bin/bash
#PBS -q bigmem
#PBS -l select=1:ncpus=55:mem=290GB
#PBS -l walltime=168:00:00
#PBS -W group_list=x-ccast-prj-hulke
#PBS -N Minimap2Mutagenesis
#PBS -j oe

# Load necessary modules (adjust as needed for your HPC)
module load samtools

# Set up working directory
cd $PBS_O_WORKDIR

# Define paths
MINIMAP2="/mmfs1/home/brian.smart/projects/Software/minimap2-2.28_x64-linux/minimap2"
REFERENCE="/mmfs1/home/brian.smart/projects/sunflower_reference_genomes/HA412HOv2_w_CPMT/Ha412HOv2_w_CPMT.fa"
HAP1="/mmfs1/home/brian.smart/projects/MutagenesisSmart/HudsonAlpha/HifiParentalIlluminaOmniCAssembly/yahs_scaffolding_trio_hap1/yahs.out_scaffolds_final_hap1.fa"
HAP2="/mmfs1/home/brian.smart/projects/MutagenesisSmart/HudsonAlpha/HifiParentalIlluminaOmniCAssembly/yahs_scaffolding_trio_hap2/yahs.out_scaffolds_final_hap2.fa"
HIFI_OMNIC="/mmfs1/home/brian.smart/projects/MutagenesisSmart/HudsonAlpha/HifiOmniCAssembly/yahs_scaffolding/yahs.out_scaffolds_final.fa"

# Function to run minimap2 and process output
run_minimap2() {
    local query=$1
    local target=$2
    local output_prefix=$3
    
    echo "Aligning $query to $target"
    $MINIMAP2 -x asm20 -t 55 --eqx -Y -c -a $target $query | tee ${output_prefix}.paf |\
    samtools view -bS - | samtools sort -@ 55 -O BAM -o ${output_prefix}.sorted.bam -
    samtools index ${output_prefix}.sorted.bam
}

# Align each assembly to the reference
run_minimap2 $HAP1 $REFERENCE "hap1_to_reference"
run_minimap2 $HAP2 $REFERENCE "hap2_to_reference"
run_minimap2 $HIFI_OMNIC $REFERENCE "hifi_omnic_to_reference"

# Align assemblies to each other
run_minimap2 $HAP1 $HAP2 "hap1_to_hap2"
run_minimap2 $HAP1 $HIFI_OMNIC "hap1_to_hifi_omnic"
run_minimap2 $HAP2 $HIFI_OMNIC "hap2_to_hifi_omnic"

echo "All alignments completed"