🐼Singularity User Guide

How to use SUMMER on hpc using singularity?

#module avial #check avialable singularity version
#First check your avaiable version of singularity on hpc and module load
module load singularity/{your_hpc_version}

#pull summer image from online:
singularity pull summer.sif docker://chuhongyuan/summer:latest

#Minimap alignment
singularity run {summersifdir}/summer.sif /opt/minimap2/minimap2 -ax map-ont --secondary=no --MD -t {number of thread} {refdir/refseq} {inputdir/inputfq.gz} -o {outputdir/output.sam}

#samtools sort and index
singularity run {summersifdir}/summer.sif opt/conda/bin/samtools view -@ {number of thread} -b {inputdir/input.sam} -o {outdir/output.bam}
singularity run {summersifdir}/summer.sif /opt/conda/bin/samtools sort -@ {number of thread} {inputdir/output.bam} -o {outdir/output_sorted.bam}
singularity run {summersifdir}/summer.sif /opt/conda/bin/samtools index -@ {number of thread} {inputdir/input_sorted.bam}

#pandepth
singularity run {summersifdir}/summer.sif /opt/PanDepth/pandepth -i {inputdir/input_sorted.bam} -o {outdir} -t {number of thread}

#call SVs
singularity run {summersifdir}/summer.sif /opt/conda/envs/cutesv/bin/cuteSV --max_cluster_bias_INS 100 --diff_ratio_merging_INS 0.3 --max_cluster_bias_DEL 100 --diff_ratio_merging_DEL 0.3 --genotype -q 20 -r 50 -L 50000000 -t {number of thread} -s 2 {inputdir/input_sorted.bam} {refdir/refseq} {outdir} {workdir}
singularity run {summersifdir}/summer.sif conda run -n svim svim alignment --min_sv_size 50 {outdir} {inputdir/input_sorted.bam} {refdir/refseq}
singularity run {summersifdir}/summer.sif conda run -n sniffles sniffles --threads {number of thread} --input {inputdir/input_sorted.bam} --vcf {outdir/sample_sniffles2.vcf} --reference {refdir/refseq}

#combisv
singularity run {summersifdir}/summer.sif perl /opt/combiSV/combiSV2.2.pl -cutesv {cutesvvcfdir/cutesvout.vcf} -svim {svimvcfdir/signatures/all.vcf} -sniffles {snifflesvcfdir/sample_sniffles2.vcf} -o {outdir/combisv.vcf}

#call STRs using straglr
singularity run {summersifdir}/summer.sif conda run -n straglr python /opt/conda/envs/straglr/bin/straglr-genotype --loci /opt/conda/envs/straglr/bin/straglr-master/repeat-annotation/hg38/merge.bed --sample sample --vcf {outdir/outdir.vcf} --sex {male OR female} {inputdir/input_sorted.bam} {refdir/refseq}

#call MEIs using tldr
singularity run {summersifdir}/summer.sif conda run -n tldr /opt/tldr/tldr/tldr -b {inputdir/input_sorted.bam} -e /opt/tldr/ref/teref.ont.human.fa -r {refdir/refseq} -n /opt/tldr/ref/nonref.collection.hg38.chr.bed.gz -p {number of thread} -o {outdir} --color_consensus

#call SNVs using clair3
singularity run {summersifdir}/summer.sif conda run -n clair3 /opt/conda/envs/clair3/bin/run_clair3.sh --bam_fn={inputdir/input_sorted.bam} --ref_fn={refdir/refseq} -t {number of thread} --platform=ont --model_path=/opt/conda/envs/clair3/bin/models/ont --output={outdir}