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Falcon unzip mechanisms #716

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mentorlg opened this issue Jul 21, 2021 · 0 comments
Open

Falcon unzip mechanisms #716

mentorlg opened this issue Jul 21, 2021 · 0 comments

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@mentorlg
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mentorlg commented Jul 21, 2021

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

@mentorlg mentorlg changed the title Difference between associated contigs and haplotigs Falcon unzip mechanisms Aug 13, 2021
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