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skingan / adapt_PurgeHaplotigs_for_FALCONPhase

Convert output of purge haplotigs to format compatible with FALCON-Phase
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Running on polished canu assembly #1

Open mccartneya90 opened 4 years ago

mccartneya90 commented 4 years ago

Hey,

I was wondering could I run this software on a polished (pilon + racon) canu assembly that I've run purge haplotigs on? And if so, do you require the initial canu assembly haplotigs file?

Thanks, A

skingan commented 4 years ago

Hi A, This was written specifically for FALCON-Unzip so I'm not sure how it would behave with canu input. You may check out the purge haplotigs code which incorporates the renaming functionality (to be compatible with FALCON-Phase). Again though, I'm not sure of the behavior with canu input.

Best, Sarah

mccartneya90 commented 4 years ago

Hi Sarah,

Thanks so much for your response on this. This was a really helpful suggestion as I had not updated my version of purge_haplotigs in awile and was not aware of this functionality. Many thanks again,

A

From: Sarah B. Kingan notifications@github.com Sent: 09 April 2020 03:35 To: skingan/adapt_PurgeHaplotigs_for_FALCONPhase adapt_PurgeHaplotigs_for_FALCONPhase@noreply.github.com Cc: Ann McCartney McCartneyA@landcareresearch.co.nz; Author author@noreply.github.com Subject: Re: [skingan/adapt_PurgeHaplotigs_for_FALCONPhase] Running on polished canu assembly (#1)

Hi A, This was written specifically for FALCON-Unzip so I'm not sure how it would behave with canu input. You may check out the purge haplotigs codehttps://bitbucket.org/mroachawri/purge_haplotigs/src/master/#markdown-header-updates which incorporates the renaming functionality (to be compatible with FALCON-Phase). Again though, I'm not sure of the behavior with canu input.

Best, Sarah

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