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benedictpaten / marginPhase

MIT License
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reference genome #10

Closed aechchiki closed 5 years ago

aechchiki commented 5 years ago

Hi @benedictpaten

thanks for delivering this tool.

We would like to see its performance for haplotyping a genome which we generated through Canu. The organism is diploid but highly heterozygous, haploid size aprox. 500Mbp. We also have the raw files (PacBio RSII).

For your pipeline to be more effective, shall I use as reference the diploid (Canu) or the haploid sequence (for now I have tested Haplomerger2 and PurgeHaplotigs post-Canu)? So I am just wondering which fasta reference to feed to your program.

Thanks, Amina

benedictpaten commented 5 years ago

Hi Amina,

I'm working on a new version of the tool that will do both assembly polishing and phasing, and my early results are very promising. But, to answer your question, you should start with the haploid sequence.

On Fri, Nov 16, 2018 at 5:51 AM Amina Echchiki notifications@github.com wrote:

Hi @benedictpaten https://github.com/benedictpaten

thanks for delivering this tool.

We would like to see its performance for haplotyping a genome which we generated through Canu https://github.com/marbl/canu. The organism is diploid but highly heterozygous, haploid size aprox. 500Mbp. We also have the raw files (PacBio RSII).

For your pipeline to be more effective, shall I use as reference the diploid (Canu) or the haploid sequence (for now I have tested Haplomerger2 https://github.com/mapleforest/HaploMerger2 and PurgeHaplotigs https://bitbucket.org/mroachawri/purge_haplotigs post-Canu)? So I am just wondering which fasta reference to feed to your program.

Thanks, Amina

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aechchiki commented 5 years ago

thanks for your answer! will use the haploid sequence then!

looking forward for your tool update, Amina