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RobertsLab / project-olympia.oyster-genomic

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Genome assembly #27

Closed ksil91 closed 7 years ago

ksil91 commented 7 years ago

Here's a paper that tested a few assemblers for hybrid analysis and chose platanus.

Here's a Biostars forum post where someone used a combination of platanus and redundans with good success.

Don't know how to tag Sean in this wiki.

sr320 commented 7 years ago

Surprisingly Sean ran into an issue with PacBio and Platanus..

https://github.com/sr320/LabDocs/issues/614

He offers some options

seanb80 commented 7 years ago

Ah! I neglected to look in here first before posting my issue. Oops!

It looks like Redundans may be an option 4 along the same likes as the DBG2OLC route. I will look in to it.

ksil91 commented 7 years ago

@seanb80 I just found out a committee member's lab uses a combination of Redundans/platanus on a mixed dataset of PacBio and Illumina mate pair on butterfly genomes. If you'd like, I can either get you in touch with their lab manager directly (she's nice) or get a copy of the parameters/pipeline they use.

seanb80 commented 7 years ago

If it isn't too much trouble, sure! I've got a good idea of what should be down, but a second se of ideas so never bad. Thanks.

On May 16, 2017, at 12:21 PM, ksil91 notifications@github.com wrote:

Just found out a committee member's lab uses a combination of Redundans/platanus on a mixed dataset of PacBio and Illumina mate pair on butterfly genomes. If you'd like, I can either get you in touch with their lab manager directly (she's nice) or get a copy of the parameters/pipeline they use.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub, or mute the thread.

sr320 commented 7 years ago

Here are some initial comparisons https://github.com/sr320/nb-2017/blob/master/O_lurida/10-Comparing-Genome-Assemblies.ipynb