[mira_talk] N50 decrease while sequencing depth increase ?
- From: "johann JOETS" <joets@xxxxxxxxxxxxxx>
- To: <mira_talk@xxxxxxxxxxxxx>
- Date: Mon, 3 Aug 2009 18:00:51 +0200
Dear Bastien,
In order to have a better view about what sequencing strategy to retain for
a piece of plant genome, I undertook some simulation work.
First I created a 150 kb sequence with RANDNA (GC% 46%). A dot plot analysis
did not show any repeated fragment.
Next I simulated 454 reads using the metasim software. I simulated 5X, 10X,
15X 25X 50X and 100X datasets and then I subjected them to assembly with
Mira.
Parameters were -job=denovo,genome,normal,454 -notraceinfo -noclipping
The N50 is as follow :
N50 av cov
5X 257 0
10X 5419 8,95
15X 111471 13,74
20X 108664 18,29
25X 27526 22,21
50X 446 40,08
You may notice that the average coverage is roughly as expected. However I
was surprised by the decrease of n50 for datasets deeper than 15X. This is
also true for the length of the largest contig.
As I know were reads should have been assembled I can check assembly quality
(roughly I count breakages in contigs). According to these tests, the
quality of the assembly also drop down.
maybe I made something wrong using Mira ?
Hope you will have an idea about this.
Many thanks for your help.
Johann
--
You have received this mail because you are subscribed to the mira_talk mailing
list. For information on how to subscribe or unsubscribe, please visit
http://www.chevreux.org/mira_mailinglists.html
Other related posts:
