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Data released on December 03, 2015

AsmVar: tools and exemplar data.

Huang, S; Krogh, A; Liu, S; Rao, J; Schierup, M, H; The Genome Denmark Consortium, ; Wang, J; Ye, W; Villesen, P; Xu, X; Li, N; Kristiansen, K; Soerensen, T, I; Hansen, T; Pedersen, O; Brunak, S; Gupta, R; Lund, O; Rasmussen, S; Bolund, L; Borglum, A, D; Eiberg, H; Flindt, E, N; Xu, R; Sun, J; Liu, H; Besenbacher, S; Grove, J; Als, T, D; Lescai, F; Mailund, T; Friborg, R, M; Pedersen, C, N; Chang, Y; Li, S; Guo, X; Cao, H; Ye, C; Maretty, L; Sibbesen, J, A; Albrechtsen, A; Bork-Jensen, J; Have, C, T; Izarzugaza, J, M; Belling, K; Yadav, R (2015): AsmVar: tools and exemplar data. GigaScience Database. http://dx.doi.org/10.5524/100173 RIS BibTeX Text

Comprehensive characterization of genomic variation in a human individual is important for understanding disease and for development of personalized approaches to treatment. Many tools exist for identification of single nucleotide polymorphism (snps), small indels and large deletions based on DNA re-sequencing strategy. However, those approaches consistently display significant bias for recovery of complex structural variants and novel sequence in the individual genomes and lack sequence interpretation such as ancestral state and mechanism. Here we present a novel approach implemented in a single software package, AsmVar, to discover, genotype and characterize different forms of structural variants and novel sequence in population-scale de novo assemblies at single nucleotide resolution. Our approach displays good scalability and makes it applicable for investigations in large population studies of species with complex genomes, such as homo sapiens. Application of AsmVar to several human de novo assemblies captures a wide spectrum of structural variants and novel sequences present in the human population with high sensitivity and specificity. Our method provides a direct solution to investigate the structural variations and novel sequences from de novo assemblies, which is important for construction of population-scale pan genome. Our study also suggests the advantages of the de novo assembly strategy for definition of genome structure.
This software has been released under the MIT License Copyright 2014-2015.

Contact Submitter

Related manuscripts:

doi:10.1186/s13742-015-0103-4

Additional information:

https://github.com/bioinformatics-centre/AsmVar

Software

http://gigadb.org/images/data/cropped/100173.jpg

Funding:

  • Funding body - Danish National Advanced Technology Foundation
  • Funding body - Danish National Research Foundation
  • Funding body - Novo Nordisk UK Research Foundation
  • Funding body - State Key Development Program for Basic Research of China-973 Program
  • Location - China

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
NA128789606HumanhumanHomo sapiens Ethnicity:Caucasian
Cell type:B-lymphocyte
Cell line:GM12878
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Displaying 1-1 of 1 Sample(s).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
File Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDFile TypeFile FormatSizeRelease Date 
Softwarezip25.25 MB2015-10-27
NA12878Otherzip80.35 MB2015-10-27
ReadmeTEXT2.59 KB2015-10-27
Displaying 1-3 of 3 File(s).

History:

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