Falcon unzip mechanisms

[mentorlg]

Dear developer,

I have some questions about Falcon and Falcon-Unzip.

1. In Falcon-Unzip, raw reads are mapped to Falcon's primary contigs to identify SNPs.
   and, using SNP information, Falcon-Unzip partitions the raw reads into each haplotype.

   If what I described above is right, is it correct that only identified heterozygosity regions (associated contig region + expanded to containing several SNPs regions) are reconstructed with phased reads (not whole graph reconstruction)...?

2. Does Falcon-Unzip use SNPs and SVs to correct unphased blocks in primary contigs...? or just use only SNPs information..?

3. In Falcon-Unzip, raw reads are phased using SNP information and update heterozygous region in assembly graph using them. If then, do I need to use the sequencing reads data (used in Falcon assembler) for input files of Falcon-Unzip..?

I look forward to your reply :)
Sincerely,
Amelia

[pb-cdunn]

Relates to PacificBiosciences/FALCON#716