Closed ksil91 closed 7 years ago
Surprisingly Sean ran into an issue with PacBio and Platanus..
https://github.com/sr320/LabDocs/issues/614
He offers some options
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.
@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.
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.
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Here are some initial comparisons https://github.com/sr320/nb-2017/blob/master/O_lurida/10-Comparing-Genome-Assemblies.ipynb
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.