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PacificBiosciences / FALCON_unzip

Making diploid assembly becomes common practice for genomic study
BSD 3-Clause Clear License
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fc_quiver and phasing #101

Closed a-velt closed 6 years ago

a-velt commented 6 years ago

Dear PacBio team,

I would like to test different alignment parameters with blasr and then polish my assembly directly with Quiver without using the fc_quiver.py script. But I have a question. My main goal is to keep the phase of my genome and I would like to know if the fc_quiver.py script participates in this step of phasing? Or only fc_unzip participates in this step of phasing ?

Thank you. Best, Amandine

a-velt commented 6 years ago

Dear PacBio team,

I don't know if someone has the answer of my question ?

Thank you very much. Best, Amandine

mroach-awri commented 6 years ago

I believe fc_unzip does the phasing, and unzip's quiver step will only map the phased reads. If you map your subreads to the diploid assembly (concatenated primary contigs and haplotigs) and polish then you should maintain the phasing.

a-velt commented 6 years ago

Thank you, this is what I did.

mictadlo commented 6 years ago

@a-velt Did it work for you to do it without fc_quiver.py?