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Stomoxys_calcitrans-1.0.1

Organism name:
Stomoxys calcitrans (stable fly)
Infraspecific name:
Breed: 8C7A2A5H3J4
Sex:
male
BioSample:
SAMN03486548
BioProject:
PRJNA188117
Submitter:
Glossina Genomes Consortium
Date:
2015/05/31
Assembly level:
Scaffold
Genome representation:
full
RefSeq category:
representative genome
GenBank assembly accession:
GCA_001015335.1 (latest)
RefSeq assembly accession:
GCF_001015335.1 (latest)
RefSeq assembly and GenBank assembly identical:
yes
WGS Project:
LDNW01
Assembly method:
ALLPATHS-LG v. April 2015
Genome coverage:
66x
Sequencing technology:
Illumina

IDs: 343881 [UID] 1789608 [GenBank] 1856038 [RefSeq]

See Genome Information for Stomoxys calcitrans

History (Show revision history)

Comment


 Background: Multiple male (F7 generation from inbred line 8C7A2A5H3J4) individual DNA isolates were provided as a pool in TE buffer for stable fly Stomoxys calcitrans courtesy of Dr. Pia Olafson, USDA. 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 approx. 10 male individuals. Various assembly metrics are summarized below. Total assembled sequence coverage of Illumina instrument reads was 66X (overlapping reads 39x, 2kb PE 24.5x, 6kb PE 2.5x) using a genome size estimate of 900Mb using the ALLPATHS-LG software (Broad Institute). This first draft assembly was referred to as S_calcitrans 1.0. In the S_calcitrans 1.0 assembly small scaffold gaps were closed with Illumina read mapping and local assembly, and scaffolding was improved using SSPACE (Boetzer 2011). 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 1.0.1 assembly. The S_calcitrans 1.0.1 assembly is made up of a total of 12,042 scaffolds with an N50 scaffold length of over 459kb (N50 contig length was 11kb). The total scaffold assembly including gaps and single contigs scaffolds spans over 971Mb. 
 For questions regarding this Stomoxys calcitrans assembly please contact Dr. Wesley Warren, Washington University School of Medicine (wwarren@genome.wustl.edu) or Dr. Pia Olafson, USDA-ARS (Pia.Olafson@ARS.USDA.gov). Downloads of the sequence data are available via the NCBI SRA database. Funding for the sequence characterization of the Stomoxys calcitrans was provided by the National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH).
 Credits:
 This work was supported by NIH-NHGRI grant 5U54HG00307907 to RKW, Director of The Genome Institute at Washington University.
 DNA source - Dr. Pia Olafson, USDA-ARS, Knipling Bushland U.S. Livestock Insects Research Lab 2700 Fredericksburg Road Kerrville, TX 78028
 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 Stomoxys calcitrans sequence assembly acknowledge Dr. Pia Olafson 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: 125702 Total contig bases: 820674819 bp Average contig length: 6529 bp Maximum contig length: 173662 bp N50 contig length: 11309 bp N50 contig number: 19213 
 *** Contiguity: Supercontig *** Total supercontig number: 12042 Average supercontig length: 68151 bp Maximum supercontig length: 3139394 bp N50 supercontig length: 459012 bp N50 supercontig number: 473 
 *** Scaffold Distribution *** Scaffolds > 1M: 134 Scaffold 250K--1M: 816 Scaffold 100K--250K: 860 Scaffold 10--100K: 2395 Scaffold 5--10K: 1038 Scaffold 2--5K: 2786 Scaffold 0--2K: 4013  more

Global statistics

Total sequence length971,188,624
Total assembly gap length150,513,805
Gaps between scaffolds0
Number of scaffolds12,042
Scaffold N50504,651
Scaffold L50509
Number of contigs125,702
Contig N5011,309
Contig L5019,213
Total number of chromosomes and plasmids0
Number of component sequences (WGS or clone)125,702

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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
unplaced971,188,62412,042820,674,819504,651113,6600
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