Final - areed37/Andrew_Reed_EPP_531 GitHub Wiki

bash /pickett_shared/software/3d-dna-201008/finalize/finalize-output-w-stats.sh \
        -c 14 \
        -s 15000 \
        -l Redbud_40x_hap1_filtered \
        Redbud_40x_hap1_filtered.final.cprops \
        Redbud_40x_hap1_filtered.final.asm \
        Redbud_40x_hap1_filtered.final.fasta \
        final \
        >& Redbud_40x_hap1_filtered.3d_dna_final.out

bash /pickett_shared/software/3d-dna-201008/finalize/finalize-output-w-stats.sh \
        -c 14 \
        -s 15000 \
        -l Redbud_40x_hap2_filtered \
        Redbud_40x_hap2_filtered.final.cprops \
        Redbud_40x_hap2_filtered.final.asm \
        Redbud_40x_hap2_filtered.final.fasta \
        final \
        >& Redbud_40x_hap2_filtered.3d_dna_final.out

minimap2 -ax asm5 -t 5 Redbud_40x_hap1_filtered.fasta Redbud_40x_hap2_filtered.fasta > hap1-vs-hap2.sam

spack load /r67sol
samtools view -b -@ 1 hap1-vs-hap2.sam > Redbud_40x_hap1-vs-hap2.bam

## Delete the SAM file to save space

rm hap1-vs-hap2.sam

singularity exec -B $PWD /sphinx_local/images/syri_1.6.3--py38hdbdd923_2.sif syri\
 -c Redbud_40x_hap1-vs-hap2.bam\
 -r Redbud_40x_hap1_filtered.final.fasta\
 -q Redbud_40x_hap2_filtered.final.fasta\
 -F B --cigar --nc 3