Format

Download Assemblies

Send to:

Choose Destination

M_pentadactyla-1.1.1

Organism name:
Manis pentadactyla (Chinese pangolin)
Isolate:
MPE899
Sex:
female
BioSample:
SAMN01943338
BioProject:
PRJNA20331
Submitter:
Washington University (WashU)
Date:
2014/08/11
Synonyms:
manPen1
Assembly level:
Scaffold
Genome representation:
full
RefSeq category:
representative genome
GenBank assembly accession:
GCA_000738955.1 (latest)
RefSeq assembly accession:
n/a
RefSeq assembly and GenBank assembly identical:
n/a
WGS Project:
JPTV01
Assembly method:
SOAPdenovo v. May 2014
Genome coverage:
61x
Sequencing technology:
Illumina

IDs: 203041 [UID] 1187128 [GenBank]

See Genome Information for Manis pentadactyla

History (Show revision history)

Comment

Background:
DNA used for sequencing the Chinese Pangolin, Manis pentadactyla, provided courtesy of Dr. Stephen O'Brien, St. Petersburg State University, was derived from a single female animal, sample ID MPE899, collected in Taiwan. The sequencing plan followed the recommendations provided ... in the SOAPdenovo assembler manual. This model requires 45x sequence coverage each of 200-300bp short inserts and 15x 3kb paired end (PE) reads as well as 5x coverage of 8kb PE reads. 
Total assembled sequence coverage of Illumina instrument reads was 61x (200-300bp short inserts, 3kbs, and 8kbs) using a genome size estimate of 2.6Gb. The first draft assembly was performed with SOAPdenovo v1.0.5 (BGI) and was referred to as M. pentadactyla 1.0. In the M. pentadactyla 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 last step in preparation for submitting the final 1.1.1 assembly. 
The M. pentadactyla 1.1.1 assembly is made up of a total of 92,722 scaffolds with an N50 scaffold length of 113,744 (N50 contig length was 28,718). Including gaps, the total assembly spans over 2.3Gb. 

For questions regarding this Chinese Pangolin 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. Funding for the sequence characterization of the Chinese Pangolin was provided by the National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH).

DNA samples can be obtained from:

Smithsonian Conservation Biology Institute
National Zoological Park
1500 Remount Road, Front Royal, VA 22630
http://www.nationalzoo.si.edu/scbi/

Credits:

This work was supported by NIH-NHGRI grant 5U54HG00307907 to RKW, Director of The Genome Institute at Washington University.

DNA source - Dr. Stephen O'Brien, St. Petersburg State University

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 Manis pentadactyla 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: 230930
Total contig bases: 1999057008 bp
Average contig length: 8657 bp
Maximum contig length: 292755 bp
N50 contig length: 28718 bp
N50 contig number: 19546

*** Contiguity: Supercontig ***
Total supercontig number: 92772
Average supercontig length: 21548 bp
Maximum supercontig length: 1231427 bp
N50 supercontig length: 113744 bp
N50 supercontig number: 4960

*** Scaffold Distribution ***
Scaffolds > 1M: 1
Scaffold 250K--1M: 1024
Scaffold 100K--250K: 4942
Scaffold 10--100K: 20199
Scaffold 5--10K: 3026
Scaffold 2--5K: 3182
Scaffold 0--2K: 60398

  more

Global statistics

Total sequence length2,204,732,179
Total assembly gap length205,675,171
Gaps between scaffolds0
Number of scaffolds92,772
Scaffold N50117,920
Scaffold L505,268
Number of contigs230,930
Contig N5028,718
Contig L5019,546
Total number of chromosomes and plasmids0
Number of component sequences (WGS or clone)230,930

Supplemental Content

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

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
unplaced2,204,732,17992,7721,999,057,008117,920138,1580
Support Center