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Glossina_brevipalpis_1.0.3

Organism name:
Glossina brevipalpis (tsetse fly)
Sex:
female
BioSample:
SAMN02742631
BioProject:
PRJNA182187
Submitter:
Glossina Genomes Consortium
Date:
2014/05/08
Assembly level:
Scaffold
Genome representation:
full
RefSeq category:
representative genome
GenBank assembly accession:
GCA_000671755.1 (latest)
RefSeq assembly accession:
n/a
RefSeq assembly and GenBank assembly identical:
n/a
WGS Project:
JFJS01
Assembly method:
ALLPATHS-LG v. August 2013
Genome coverage:
81x
Sequencing technology:
Illumina

IDs: 178391 [UID] 1069188 [GenBank]

See Genome Information for Glossina brevipalpis

History (Show revision history)

Comment

Background: A total of 10 female individual DNA isolates were provided as a pool in TE buffer for tsetse fly Glossina brevipalpis 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 approximately 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 10 female individuals. Various assembly metrics are summarized below. Total assembled sequence coverage of Illumina instrument reads was 81X (overlapping reads 61x, 2.1kb PE 14x, 4.3kb PE 6x) using a genome size estimate of 400Mb using the ALLPATHS-LG software (Broad Institute). This first draft assembly was referred to as G. brevipalpis 1.0. In the G. brevipalpis 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. brevipalpis 1.0.3 assembly is made up of a total of 1651 scaffolds with an N50 scaffold length of over 1.2Mb (N50 contig length was 62kb). The total contigs assembly spans 295Mb. 
 For questions regarding this G. brevipalpis 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 brevipalpis 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 brevipalpis 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: 16658 Total contig bases: 293469513 bp Average contig length: 17617 bp Maximum contig length: 1227313 bp N50 contig length: 62009 bp N50 contig number: 981
 *** Contiguity: Supercontig *** Total supercontig number: 1651 Average supercontig length: 177753 bp Maximum supercontig length: 10047545 bp N50 supercontig length: 1229952 bp N50 supercontig number: 59
 *** Scaffold Distribution *** Scaffolds > 1M: 76 Scaffold 250K--1M: 188 Scaffold 100K--250K: 128 Scaffold 10--100K: 256 Scaffold 5--10K: 91 Scaffold 2--5K: 172 Scaffold 0--2K: 740  more

Global statistics

Total sequence length315,360,362
Total assembly gap length21,890,849
Gaps between scaffolds0
Number of scaffolds1,651
Scaffold N501,209,507
Scaffold L5063
Number of contigs16,658
Contig N5062,009
Contig L50981
Total number of chromosomes and plasmids0
Number of component sequences (WGS or clone)16,658

Supplemental Content

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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
unplaced315,360,3621,651293,469,5131,209,50715,0070
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