
prerequisite:BWA/0.7.17 minimap2 samtools

You may download reference hg19 v2.1.0 from here. 
```wget https://cf.10xgenomics.com/supp/genome/refdata-hg19-2.1.0.tar.gz
tar -xzvf refdata-hg19-2.1.0.tar.gz
```

HG002-T2T.v1.1.fasta
```
wget https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/HG002/assemblies/hg002v1.1.fasta.gz
```

strand seq data
```
${aws} s3 cp s3://human-pangenomics/NHGRI_UCSC_panel/HG002/hpp_HG002_NA24385_son_v1/Strand_seq/ ./ --recursive --no-sign-request
```

Then run command below.
```
strandseq_download_dir=<strand seq>
ASM_HG002_T2T=<ASM_HG002_T2T>
reference_hg19=<ref_hg19>
ASM_DIR_HG002_FocalSV=zenodo/HG002_ASM_FocalSV/Hifi_L1_FocalSV-auto

cd 1-strand-seq_reads
sh 1-strand-seq_reads.sh ${strandseq_download_dir}
cd ..

cd 2-align_to_T2T-HG002
sh 2-align_to_T2T-HG002.sh ${ASM_HG002_T2T}
cd ..


cd 3-align_T2T-HG002_to_ref
sh 3-align_T2T-HG002_to_ref.sh ${reference_hg19} ${ASM_HG002_T2T}
cd ..


cd 4-align_to_PhaseBlock
sh 4-align_to_PhaseBlock.sh ${ASM_DIR_HG002_FocalSV} ${reference_hg19} ${ASM_HG002_T2T}
cd ..
```

