Carrot Genome Assembly DCARv1 Gap Fill

Resource Type: 
Carrot Genome Assembly DCARv1 Gap Fill

This analysis represents one step of the whole genome assembly process, the gap fill process. This is described in section 1.3.1 of the Supplementary Note of the referenced publication.

Gaps were filled using GapCloser for SOAPdenovo which uses the paired-end information to retrieve the read pairs in which one end is mapped to the unique contig and the other is located within a gap region. These read pairs are then used to perform a local assembly to fill gaps. The result was designated carrot assembly v1.0, which resulted in 4,182 scaffolds covering 418 Mb with an N50 (50% of the genome is in fragments of this length or longer) of 8.073×105nt and 3,914 contigs covering 5.4×106nt with an N50 of 1.8×103nt. Scaftigs covered 3.906×105nt with an N50 of 3.11×104nt.

Data from this analysis can be viewed in JBrowse here.

Iorizzo M, Ellison S, Senalik D, Zeng P, Satapoomin P, Huang J, Bowman M, Iovene M, Sanseverino W, Cavagnaro P, Yildiz M, Macko-Podgórni A, Moranska E, Grzebelus E, Grzebelus D, Ashrafi H, Zheng Z, Cheng S, Spooner D, Van Deynze A, Simon P. A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution.. Nature genetics. 2016 06; 48(6):657-66.
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The analysis, Carrot Genome Assembly DCARv1 Gap Fill, is a part of analysis, Carrot Genome Assembly DCARv2.
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Program, Pipeline, Workflow or Method Name: 
GapCloser for SOAPdenovo
Program Version: 
not specified
Date Performed: 
Tuesday, March 31, 2015 - 00:00
Data Source: 
Source Name
NameCommon NameComment
For a general overview of carrot, see the Carrot Facts Page
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