How to use Falcon output with Falcon_unzip and SMRT-analysis to get Phased Diploid Genome Assembly?

[ls2017]

I am completely new to PacBio data analysis and we are doing Phased Diploid Genome assembly.

We have got 13 SMRT cell reads for one sample and I have successfully run Falcon, which generated the 3 output folders 0-rawreads, 1-preads_ovl, and 2-asm-falcon.

I have also installed Falcon_unzip and SMRT-analysis.

Under the folder FALCON_unzip-master/examples, there are 2 files: unzip.sh and fc_unzip.cfg

The contents of unzip.sh is as the following: fc_unzip.py fc_unzip.cfg fc_quiver.py fc_unzip.cfg

The fc_unzip.cfg is as below: [General] job_type = SGE

[Unzip] input_fofn= input.fofn input_bam_fofn= input_bam.fofn

smrt_bin=/mnt/secondary/builds/full/3.0.0/prod/current-build_smrtanalysis/smrtcmds/bin/

jobqueue = your_sge_queue sge_phasing= -pe smp 12 -q %(jobqueue)s sge_quiver= -pe smp 12 -q %(jobqueue)s sge_track_reads= -pe smp 12 -q %(jobqueue)s sge_blasr_aln= -pe smp 24 -q %(jobqueue)s sge_hasm= -pe smp 48 -q %(jobqueue)s unzip_concurrent_jobs = 64 quiver_concurrent_jobs = 64

My Question 1: shall I just supply input.fofn and input_bam.fofn to run the command: unzip.sh fc_unzip.cfg?

My Question 2: How can I generate input_bam.fofn?

My Question 3: Does the input.fofn contain the path and names of all the *.bax.h5 files?

My Question 4: Do I need to worry about using the following SMRT commands with settings.xml as mentiond below? If so, where and how to get settings.xml? $ $SMRT_ROOT/current/etc/setup.sh $ smrtpipe.py params=settings.xml xml:input.xml