long-range technologies for genome scaffolding

ybukhman · 02-09-2018, 01:12 PM

Hi all,

I am working on a mammalian genome project. We have an assembly from PacBio reads with N50 = 6.2 Mb. We would like to generate some long-range data that could be used for scaffolding. I am aware of several options, including Nanopore, Hi-C (with Dovetail or Phase Genomics), optical maps (Bionano), and synthetic long reads (10X). Can you share your experiences with these technologies? We need help choosing which one(s) to use.

Thanks.

Yury

nucacidhunter · 02-09-2018, 05:22 PM

You already have a good N50 with long reads. The options are combination of 10x Link reads, Hi-C and optical mapping. Searching " Vertebrate Genomes Project Plans to Combine Technologies for 'Near Gapless' Assemblies" should give more ideas but you might be asked to create an account to access it.

ybukhman · 02-10-2018, 08:48 AM

Thanks for the tip, nucacidhunter!

JTH-Genome · 04-09-2019, 06:59 AM

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!

If your budget is tight, I would add HiC data from Phase Genomics or Arima Genomics. If phasing information is important, then add some 10X Genomics data (https://www.10xgenomics.com/solutions/assembly/).

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02-09-2018, 01:12 PM	#1
ybukhman Junior Member Location: Madison, WI, USA Join Date: Jan 2011 Posts: 6	long-range technologies for genome scaffolding Hi all, I am working on a mammalian genome project. We have an assembly from PacBio reads with N50 = 6.2 Mb. We would like to generate some long-range data that could be used for scaffolding. I am aware of several options, including Nanopore, Hi-C (with Dovetail or Phase Genomics), optical maps (Bionano), and synthetic long reads (10X). Can you share your experiences with these technologies? We need help choosing which one(s) to use. Thanks. Yury

04-09-2019, 06:59 AM	#4
JTH-Genome Junior Member Location: USA, NC Join Date: Apr 2019 Posts: 6	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! If your budget is tight, I would add HiC data from Phase Genomics or Arima Genomics. If phasing information is important, then add some 10X Genomics data (https://www.10xgenomics.com/solutions/assembly/).

02-09-2018, 05:22 PM	#2
nucacidhunter Jafar Jabbari Location: Melbourne Join Date: Jan 2013 Posts: 1,230	You already have a good N50 with long reads. The options are combination of 10x Link reads, Hi-C and optical mapping. Searching " Vertebrate Genomes Project Plans to Combine Technologies for 'Near Gapless' Assemblies" should give more ideas but you might be asked to create an account to access it.

02-10-2018, 08:48 AM	#3
ybukhman Junior Member Location: Madison, WI, USA Join Date: Jan 2011 Posts: 6	Thanks for the tip, nucacidhunter!