Drosophila takahashii

Overview

As part of the Drosophila modENCODE project, the Baylor College of Medicine is studying the comparative genomics of eight additional species of Drosophila: biarmipes, bipectinata, elegans, eugracillis, ficusphila, kikkawai, rhopaloa, and takahashii.

Please cite the following publication when using the D. takahashii genome and annotations:
Chen, Z. X., Sturgill, D., Qu, J., et al. Comparative validation of the D. melanogaster modENCODE transcriptome annotation. Genome research, 2014, 24(7), 1209-1223. doi: 10.1101/gr.159384.113


Image Credit: Nicolas Gompel. View Source. CC BY-NC-SA 3.0
Organism Image
Feature Summary
The following features are currently present for this organism
Feature TypeCount
CDS55,430
mRNA13,507
Gene13,507
Contig N50
125250
Scaffold N50
387609
Number Of Genes
13507
Image Credit
Nicolas Gompel. <a href="http://gompel.org/wp-content/gallery/drosophilidae/Drosophila-Sophophora-takahashii-NCBSisoFline01_plate_small.jpg">View Source.</a> <a href="https://creativecommons.org/licenses/by-nc-sa/3.0/">CC BY-NC-SA 3.0</a>

Assembly Information

Analysis Name Whole Genome Assembly of Drosophila takahashii provided by the Baylor College of Medicine
Software Baylor College of Medicine genome assembly pipeline
Source Drosophila takahashii Dtak02082011 assembly
Date performed 2013-07-30
Materials & Methods

From http://www.ncbi.nlm.nih.gov/nuccore/AFFI00000000.2/:

This is an upgrade of the Dtak_1.0 assembly using illumina reads to fix indels and other improvements using BWA, samtools etc. Not a traditional assembler.

Assembly Method:

Celera Assembler v. 6.1; BWA v. 0.6.0; Samtools v. 0.1.14; GATK v. 1.1-9; Indel_call_and_upgrade.pl v. 1.0

Assembly Name: Dtak_2.0

Genome Coverage: 242.1x

Sequencing Technology: 454; Illumina GAIIx

Statistics

Assembly Metrics
Contig N50 125250
Scaffold N50 387609
GC Content 40.15