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C_hoffmanni-2.0.1

Organism name:
Choloepus hoffmanni (Hoffmann's two-fingered sloth)
Isolate:
OR478-KB4484
Sex:
female
BioSample:
SAMN02146716
Submitter:
The Genome Institute, Washington University School of Medicine
Date:
2014/09/30
Assembly level:
Scaffold
Genome representation:
full
RefSeq category:
representative genome
GenBank assembly accession:
GCA_000164785.2 (latest)
RefSeq assembly accession:
n/a
RefSeq assembly and GenBank assembly identical:
n/a
WGS Project:
ABVD02
Assembly method:
MaSuRCA v. May 2014
Genome coverage:
65x
Sequencing technology:
Illumina

IDs: 215251 [UID] 1341598 [GenBank]

See Genome Information for Choloepus hoffmanni

History (Show revision history)

Comment

Background: The Hoffmann's Two-toed sloth, Choloepus hoffmanni, was selected by NHGRI for sequencing to inform the human genome through comparative genomics. Sequencing the genomes of diverse organisms such as the sloth, is a powerful tool to better understand biological ... processes at work in human health and illness. Interestingly, recent research, published in the scientific journal PLoS One, says that sloth hairs contain compounds that can be used against bacteria, breast cancer cells and the parasites that cause malaria and Chagas disease. The sloth belongs to the superorder Xenarthra, which includes anteaters and armadillos. DNA used for sequencing the Hoffmann's Two-toed sloth provided, by the San Diego Zoo Institute for Conservation Research, was derived from a single female (OR478-KB4484) that was born in the wild, but for which birth location is uncertain. The sequencing/assembly strategy utilized Sanger 3730 (ABI) and Illumina reads. The coverages used included 
3X of Sanger reads, and 60X of Illumina reads. The Illumina reads consisted of 30X of fragment, 15X of 3 Kb PE, and 15X of 8 Kb PE reads. Total assembled sequence coverage of the instrument data was 65X using a genome size estimate of 3.3Gb. The first TGI draft assembly was performed with MaSuRCA (Zimin et al 2013) and was referred to as C. hoffmanni 2.0. In the C. hoffmanni 2.0 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. All scaffolds (singletons) and contigs within scaffolds that were 200bp and less in length were removed from the assembly. Removing these contigs was the last step in preparation for submitting the final 2.0.1 assembly. The C. hoffmanni 2.0.1 assembly is made up of a total of 269K scaffolds with an N50 scaffold length nearly 364 Kb (N50 contig length was 64.5 Kb). The total contig assembly spans over 3.2 Gb. 
 For questions regarding this Hoffmann's Two-toed sloth assembly please contact Dr. Wesley Warren, Washington University School of Medicine (wwarren@genome.wustl.edu). Downloads of the sequence data are available via the NCBI SRA database. 
 This work was supported by NIH grant HG003079 to Richard K. Wilson, Washington University School of Medicine.
 DNA samples can be obtained from: 
 Biomaterials Review Group San Diego Zoo Institute for Conservation Research 15600 San Pasqual Valley Road Escondido, California 92027
 or by emailing: biomaterialsreviewgroup@sandiegozoo.org
 Credits:
 DNA source - Dr. Oliver Ryder, San Diego Zoo Institute for Conservation Research
 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, and Aleksey Zimin, IPS&T, University of Maryland, College Park, MD.
 Citation upon use of this assembly in a manuscript: 
 It is requested that users of this Choloepus hoffmanni sequence assembly acknowledge Dr. Richard K. Wilson 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: 370041 Total contig bases: 3223352558 bp Average contig length: 8711 bp Maximum contig length: 711720 bp N50 contig length: 64490 bp N50 contig number: 13390
 *** Contiguity: Supercontig *** Total supercontig number: 269084 Average supercontig length: 11979 bp Maximum supercontig length: 3323232 bp N50 supercontig length: 363844 bp N50 supercontig number: 2401
 *** Scaffold Distribution *** Scaffolds > 1M: 301 Scaffold 250K--1M: 3339 Scaffold 100K--250K: 3149 Scaffold 10--100K: 13894 Scaffold 5--10K: 9091 Scaffold 2--5K: 17154 Scaffold 0--2K: 222156  more

Global statistics

Total sequence length3,286,013,499
Total assembly gap length62,660,941
Gaps between scaffolds0
Number of scaffolds269,084
Scaffold N50366,442
Scaffold L502,423
Number of contigs370,041
Contig N5064,490
Contig L5013,390
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
unplaced3,286,013,499269,0843,223,352,558366,442100,9570