In the README of quickmerge, I got a advice.

Assembly polishing with Quiver and pilon before and after assembly merging is strongly recommended.

As for Sequal data, Pacbio updated the quiver to arrow.

Quiver is supported for PacBio RS data. Arrow is supported for PacBio Sequel data and RS data with the P6-C4 chemistry.

So, let’s do it !

Step 0 Install SMRT Tools

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SMRT_ROOT=/opt/pacbio/smrtlink
./smrtlink_5.1.0.26412.run --rootdir $SMRT_ROOT --smrttools-only

SMRT tools will be installed in /opt/pacbio/smrtlink/smrtcmds/bin , add this directory into your PATH bash variable.

Step 0.5 Convert row bax file into scraps.bam (RS data)

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bax2bam -f $FOFN -o $BAM_DIR"/SMRT-cell-"$COMPT --subread  --pulsefeatures=DeletionQV,DeletionTag,InsertionQV,IPD,MergeQV,SubstitutionQV,PulseWidth,SubstitutionTag

Step 0.8 Convert scraps.bam to subreads.bam

Step 1 Align subreads.bam

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pbalign --nproc 16 xxx.bam reference.fasta align_xxx.bam

Step 2 Sort bam files

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## Sort alignments by leftmost coordinates, or by read name when -n is used.
samtools sort [-@ threads] [-m max memory per threads] align_xxx.bam -o align_xxx.sort.bam

Step 3 Merge all the produced bam files

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samtools merge <align_xxx.merge.sort.bam> <in1.bam> <in2.bam> [...]

Step 4 Index the input files

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## Index a coordinate-sorted BAM or CRAM file for fast random access
samtools index align_xxx.merge.sort.bam
pbindex align_xxx.merge.sort.bam
## Index reference sequence in the FASTA format 
samtools faidx reference.fasta

Step 5 VariantCaller: arrow

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arrow -j 16 --maskRadius 3 \
aligned_xxx.merge.sort.bam \
-r reference.fasta \
-o variants.gff -o myConsesus.fasta -o myConsesus.fastq

Reference

https://www.biostars.org/p/273447

https://www.pacb.com/wp-content/uploads/SMRT-Tools-Reference-Guide-v4.0.0.pdf