Carrot Genome Assembly DCARv1 Gap Fill

Resource Type:

Analysis

Name:

Description:

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.

File:


File	Type
DCARv2 Filled Gaps JBrowse GFF3	GFF3

Publication:

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.

Relationship:

There is 1 relationship.
Relationships
The analysis, Carrot Genome Assembly DCARv1 Gap Fill, is a part of analysis, Carrot Genome Assembly DCARv2.

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: : BGI

Organism:


Name	Common Name	Comment
Daucus carota subsp. sativus	Carrot	For a general overview of carrot, see the Carrot Facts Page