[mira_talk] Re: a question about Nextera Kit vs TruSeq Kit

  • From: Kevin Chen <wchen20@xxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Wed, 29 Oct 2014 12:16:51 -0400

Nextera XT uses 1ng gDNA or cDNA. That is a huge advantage.

Adrian, can you give more details on the coverage consistency, what metrics
you used to measure it? Thanks!

Regards,
Bing

On Wed, Oct 29, 2014 at 10:41 AM, Chris Hoefler <hoeflerb@xxxxxxxxx> wrote:

> How minute are we talking about? TruSeq Nano can start with ~100 ng
> unsheared gDNA.
>
> On Tue, Oct 28, 2014 at 7:03 PM, Kevin Chen <wchen20@xxxxxxxxx> wrote:
>
>> Hi, Bastian & Mira community
>>
>> I am Bing from U of Maryland. When I read your Mira manual, I notice this
>> statement below. I am interested in getting more information on that.
>> Because Nextera kit has its own advantages that TruSeq does not have, for
>> example, working with minute amount of material, I have high hope for
>> Nextera. Do you have any prelim data to support this statement? If this is
>> true, I have to re-think a lot of my experiment design using Nextera,
>> that’ll change a lot of things.
>>
>>
>> "For de-novo assemblies, do NOT (never ever at all and under no
>> circumstances) use the Nextera kit, take TruSeq. The non-random
>> fragmentation behaviour of Nextera leads to all sorts of problems for
>> assemblers (not only MIRA) which try to use kmer frequencies as a criterion
>> for repetitiveness of a given sequence."
>>
>> Thank you in advance,
>> Bing
>>
>>
>
>
> --
> Chris Hoefler, PhD
> Postdoctoral Research Associate
> Straight Lab
> Texas A&M University
> 2128 TAMU
> College Station, TX 77843-2128
>

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