Format

Download Assemblies

Send to:

Choose Destination

Glossina_austeni-1.0.3

Organism name:
Glossina austeni (tsetse fly)
Sex:
female
BioSample:
SAMN02768703
BioProject:
PRJNA189552
Submitter:
Glossina Genomes Consortium
Date:
2014/05/12
Assembly level:
Scaffold
Genome representation:
full
RefSeq category:
representative genome
GenBank assembly accession:
GCA_000688735.1 (latest)
RefSeq assembly accession:
n/a
RefSeq assembly and GenBank assembly identical:
n/a
WGS Project:
JMRR01
Assembly method:
ALLPATHS-LG v. August 2013
Genome coverage:
62x
Sequencing technology:
Illumina

IDs: 180591 [UID] 1085768 [GenBank]

See Genome Information for Glossina austeni

History (Show revision history)

Comment

Background: A total of 20 female individual DNA isolates were provided as a pool in TE buffer for tsetse fly Glossina austeni courtesy of Dr. Serap Aksoy, Yale University. The sequencing plan followed the recommendations provided in the ALLPATHS-LG ... assembler manual. This model requires 45x sequence coverage each of fragments (overlapping paired reads approx. 180bp length) and 3kb paired end (PE) reads as well as 5x coverage of 8kb PE reads. For fragments and all jumping libraries (3 and 8kb) we used a DNA sample pooled from 20 female individuals. Various assembly metrics are summarized below. Total assembled sequence coverage of Illumina instrument reads was 62X (overlapping reads 42x, 2.0kb PE 13x, 4.0kb PE 7x) using a genome size estimate of 400Mb using the ALLPATHS-LG software (Broad Institute). This first draft assembly was referred to as G. austeni 1.0. In the G. austeni 1.0 assembly small scaffold gaps were closed with Illumina read mapping and local assembly. Contaminating contigs, trimmed vector in the form of X's and ambiguous bases as N's in the sequence were removed. NCBI requires that all contigs 200bp and smaller be removed. Removing these contigs was the final step in preparation for submitting the 1.0.3 assembly. The G. austeni 1.0.3 assembly is made up of a total of 2205 scaffolds with an N50 scaffold length of over 798kb (N50 contig length was 46kb). The total contigs assembly spans 358Mb. 
 For questions regarding this G. austeni assembly please contact Dr. Wesley Warren, Washington University School of Medicine (wwarren@genome.wustl.edu) or Dr. Serap Aksoy, Yale University (serap.aksoy@yale.edu). Downloads of the sequence data are available via the NCBI SRA database. Funding for the sequence characterization of the Glossina austeni was provided by the National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH).
 DNA samples can be obtained from: Dr. Serap Aksoy, Department of Epidemiology of Microbial Diseases, Yale School of Public Health, 60 College St., 626 LEPH, New Haven, CT 06510
 Credits:
 This work was supported by NIH-NHGRI grant 5U54HG00307907 to RKW, Director of The Genome Institute at Washington University.
 DNA source - Dr. Serap Aksoy, Yale University, Hartford, CT. 
 Sequencing - The Genome Institute, Washington University School of Medicine, St Louis, MO. 
 Sequence assembly - The Genome Institute, Washington University School of Medicine, St Louis, MO.
 Citation upon use of this assembly in a manuscript: 

 It is requested that users of this Glossina austeni sequence assembly acknowledge Dr. Serap Aksoy and The Genome Institute, Washington University School of Medicine in any publications that result from use of this sequence assembly.
 Assembly stats:
 *** Contiguity: Contig *** Total contig number: 18631 Total contig bases: 353476734 bp Average contig length: 18973 bp Maximum contig length: 1008035 bp N50 contig length: 45924 bp N50 contig number: 1856
 *** Contiguity: Supercontig *** Total supercontig number: 2205 Average supercontig length: 160307 bp Maximum supercontig length: 5780510 bp N50 supercontig length: 798234 bp N50 supercontig number: 112
 *** Scaffold Distribution *** Scaffolds > 1M: 71 Scaffold 250K--1M: 301 Scaffold 100K--250K: 247 Scaffold 10--100K: 391 Scaffold 5--10K: 85 Scaffold 2--5K: 220 Scaffold 0--2K: 890  more

Global statistics

Total sequence length370,264,922
Total assembly gap length16,788,838
Gaps between scaffolds0
Number of scaffolds2,205
Scaffold N50812,585
Scaffold L50116
Number of contigs18,631
Contig N5045,924
Contig L501,856
Total number of chromosomes and plasmids0
Number of component sequences (WGS or clone)18,631

Supplemental Content

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Global assembly definition

Download the full sequence report
Click on the table row to see sequence details in the table to the right
Assembly Unit Name
Primary Assembly
The primary assembly unit does not have any assembled chromosomes or linkage groups.
Please download the full sequence report for information on the scaffolds.

Assembly statistics

MoleculeTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
unplaced370,264,9222,205353,476,084812,58516,4260
Support Center