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IDs: 203041 [UID] 1187128 [GenBank]
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
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