DCARv2 Filled Gaps JBrowse GFF3

Resource Type: 
File
File Type: 
GFF3
Download: 
Download File NameAvailable atSizeMD5
01.gapfill.gff3.gzCarrotOmics3.99MB8a39889b987724a61a81ac3c4389599b
Description: 

Filled gaps in the genome assembly. This is the GFF3 file used for JBrowse. See the linked analysis below for further details.

References: 
The following records refer to this file:
AnalysisLoading content
OrganismLoading content
Analysis: 
NameDescription

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.

Loading content
Organism: 
NameCommon NameComment
Carrot
For a general overview of carrot, see the Carrot Facts Page
Loading content
License: 
NamePublic Domain
License Summary

The data have no known copyrights or restrictions and can be be freely used by anyone.

Full Legal TextNot Available