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Glossina_fuscipes-3.0.2

Organism name:
Glossina fuscipes fuscipes (tsetse fly)
Sex:
female
BioSample:
SAMN02742630
BioProject:
PRJNA172853
Submitter:
Glossina Genomes Consortium
Date:
2014/05/08
Assembly level:
Scaffold
Genome representation:
full
RefSeq category:
representative genome
GenBank assembly accession:
GCA_000671735.1 (latest)
RefSeq assembly accession:
n/a
RefSeq assembly and GenBank assembly identical:
n/a
WGS Project:
JFJR01
Assembly method:
ALLPATHS-LG v. September 2013
Genome coverage:
120x
Sequencing technology:
Illumina

IDs: 178401 [UID] 1069198 [GenBank]

See Genome Information for Glossina fuscipes

History (Show revision history)

Comment

Background: A total of 6 female individual DNA isolates were provided in TE buffer for tsetse fly Glossina fuscipes 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 we used DNA samples pooled from mother and offspring named M1 and M1-2 and for all jumping libraries (3 and 8kb) we used a pool of these DNA samples MD7, MD7-2, MD8 and MD8-1. Various assembly metrics are summarized below. Total assembled sequence coverage of Illumina instrument reads was 120X (overlapping reads 72x, 3.5kb PE 41x, 4.0kb PE 7x) using a genome size estimate of 400Mb using the ALLPATHS-LG software (Broad Institute). This first working draft assembly was referred to as G.fuscipes 3.0. In the G.fuscipes 3.0 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 3.0.2 assembly. The G. fuscipes 3.0.2 assembly is made up of a total of 2395 scaffolds with an N50 scaffold length of over 555kb (N50 contig length was 64kb). The total contigs assembly spans 365Mb. 
 For questions regarding this G. fuscipes 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 fuscipes 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 fuscipes 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: 13568 Total contig bases: 361276677 bp Average contig length: 26627 bp Maximum contig length: 1242950 bp N50 contig length: 64354 bp N50 contig number: 1534

 *** Contiguity: Supercontig *** Total supercontig number: 2395 Average supercontig length: 150846 bp Maximum supercontig length: 3216142 bp N50 supercontig length: 555539 bp N50 supercontig number: 174
 *** Scaffold Distribution *** Scaffolds > 1M: 66 Scaffold 250K--1M: 375 Scaffold 100K--250K: 335 Scaffold 10--100K: 469 Scaffold 5--10K: 124 Scaffold 2--5K: 323 Scaffold 0--2K: 703  more

Global statistics

Total sequence length374,774,708
Total assembly gap length13,498,031
Gaps between scaffolds0
Number of scaffolds2,395
Scaffold N50561,190
Scaffold L50179
Number of contigs13,568
Contig N5064,354
Contig L501,535
Total number of chromosomes and plasmids0
Number of component sequences (WGS or clone)13,568

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
unplaced374,774,7082,395361,276,677561,19011,1730
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