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Forum: Sample Prep / Library Generation 06-27-2019, 10:05 AM
Replies: 3
Views: 1,250
Posted By JTH-Genome
Smile BioNano

I agree with Phillip. Use the agarose plugs for the lysis. It might be old school, but it is making a comeback! You can use the BioNano protocol for high MW DNA. It's one of the best protocols...
Forum: De novo discovery 06-27-2019, 09:55 AM
Replies: 1
Views: 1,173
Posted By JTH-Genome
You could try to modify one of these error...

You could try to modify one of these error correction algorithms: http://wgs-assembler.sourceforge.net/wiki/index.php/PBcR
Forum: Bioinformatics 04-30-2019, 03:50 AM
Replies: 12
Views: 955
Posted By JTH-Genome
Thumbs up Canine genomes

I liked GenoMax's suggestion, so go with that if you haven't already. Also be sure to use long read (PacBio) based assembly for your analysis against a reference genome.
If you are interested in...
Forum: Sample Prep / Library Generation 04-24-2019, 10:53 AM
Replies: 1
Views: 1,081
Posted By JTH-Genome
Although not ideal, try the method described in...

Although not ideal, try the method described in this paper: https://www.nature.com/articles/srep31584
Forum: De novo discovery 04-09-2019, 06:09 AM
Replies: 2
Views: 5,025
Posted By JTH-Genome
Hi Pawan, I also would highly recommend...

Hi Pawan,

I also would highly recommend Phase Genomics' HiC approach to getting telomere and centromere information. Blasting for it may be tricky since those portions generally don't assemble...
Forum: De novo discovery 04-09-2019, 05:59 AM
Replies: 3
Views: 3,087
Posted By JTH-Genome
Thumbs up Scaffolding

As nucacidhunter mentioned, I would highly recommend you work with the VGP group. I've work with the VGP and had excellent results for my de novo projects. They even do the hybrid assemblies!
...
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