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Poecilia_formosa-5.1.2

Organism name:
Poecilia formosa (Amazon molly)
Sex:
female
BioSample:
SAMN02981564
Submitter:
Aquatic Genome Models
Date:
2013/10/28
Assembly level:
Scaffold
Genome representation:
full
RefSeq category:
representative genome
GenBank assembly accession:
GCA_000485575.1 (latest)
RefSeq assembly accession:
GCF_000485575.1 (latest)
RefSeq assembly and GenBank assembly identical:
yes
WGS Project:
AYCK01
Assembly method:
AllPaths-LG v. July 2013
Genome coverage:
82x
Sequencing technology:
Illumina

IDs: 74641 [UID] 838838 [GenBank] 1008418 [RefSeq]

See Genome Information for Poecilia formosa

History (Show revision history)

Comment

Poeciliia formosa (Amazon molly) Sequence Assembly Release Notes
 The Amazon molly DNA for shotgun sequencing is derived from a adult female (Poecilia formosa; fish id Pfo_4394_1 and Pfo_4394_2) within the laboratory of Dr. Manfred Schartl at the Biocenter of ... the University of Wurzburg, Germany. Total sequence genome input coverage on the Illumina HiSeq instrument was approximately 95x (45x fragments, 45x 3kb, 5x 8kb and 0.05x 40kb), while the assembled coverage was 85x. 
 The combined sequence reads were assembled using the ALLPATHS software (Broad Institute). Two independent draft assemblies were created, both ALLPATHS with different coverage parameters, then merged with graph accordance methods (Yao et. al. 2011. Bioinformatics). The merged assembly was further improved with the external scaffolding tool SSPACE. Final steps were to align scaffolds to the platyfish chromosome reference to evaluate synteny and alignment of 3kb reads to assess mate pair discordance with REAPER. Information from both sources was used to break misassembled scaffolds when evidence was sufficient. The final draft assembly was referred to as Poeciliia formosa 5.1.2. This version has been gap filled and cleaned of contaminating contigs. The assembly is made up of a total of 3985 scaffolds with an N50 scaffold length of almost 1.6Mb (N50 contig length was 57kb). The assembly spans 714Mb. 
 This work was supported by NIH grant R24 RR032658-01 to Dr. Warren, Washington University School of Medicine.
 DNA Source Contact: Dr. Manfred Schartl, Physiological Chemistry I University of Wuerzburg Biozentrum, Am Hubland Wuerzburg 97074 Germany
 **************************************************************
 Poecillia formosa 5.1.2 Sequence and Assembly Credits:
 DNA source - Dr. Manfred Schartl, Physiologische Chemie, Biozentrum, Am Hubland, Universitat Wurzburg, Germany. Genome Sequence - The Genome Institute, Washington University School of Medicine, St Louis, MO. Sequence Assembly - The Genome Institute, Washington University School of Medicine, St Louis, MO. Assembly curation - Pat Minx, 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 Poecillia formosa 5.1.2 sequence assembly acknowledge Wesley Warren and The Genome Institute, Washington University School of Medicine in any publications that result from use of this sequence assembly. 

 Poecillia formosa 5.1.2 assembly statistics:
 *** Contiguity: Contig *** Total contig number: 31105 Total contig bases: 714206035 bp Average contig length: 22961 bp Maximum contig length: 528603 bp N50 contig length: 57472 bp N50 contig number: 3546
 *** Contiguity: Supercontig *** Total supercontig number: 4001 Average supercontig length: 178507 bp Maximum supercontig length: 7248354 bp N50 supercontig length: 1572400 bp N50 supercontig number: 125
 Scaffolds > 1M: 204 Scaffold 250K--1M: 352 Scaffold 100K--250K: 233 Scaffold 10--100K: 828 Scaffold 5--10K: 453 Scaffold 2--5K: 815 Scaffold 0--2K: 1116  more

Global statistics

Total sequence length748,923,461
Total assembly gap length34,726,196
Gaps between scaffolds0
Number of scaffolds3,985
Scaffold N501,574,226
Scaffold L50130
Number of contigs31,058
Contig N5057,472
Contig L503,547
Total number of chromosomes and plasmids0

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Global assembly definition

Download the full sequence report
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
unplaced748,923,4613,985714,197,2651,574,22627,0730