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Title: AsmVar: tools and exemplar data.      
dateReleased:
12-03-2015
privacy:
not applicable
aggregation:
instance of dataset
dateCreated:
12-03-2015
refinement:
curated
ID:
doi:10.5524/100173
creators:
,
Consortium, The Genome Denmark
Krogh, Anders
Wang, Jun
Schierup, Mikkel H
Villesen, Palle
Xu, Xun
Li, Ning
Kristiansen, Karsten
Soerensen, Thorkild I.A
Hansen, Torben
Pedersen, Oluf
Rasmussen, Simon
Lund, Ole
Bolund, Lars
Borglum, Anders D
Eiberg, Hans
Flindt, Esben N
Liu, Hao
Grove, Jakob
Als, Thomas D
Lescai, Francesco
Mailund, Thomas
Friborg, Rune M
Pedersen, Christian N.S.
Ye, Chen
Maretty, Lasse
Sibbesen, Jonas A
Albrechtsen, Anders
Bork-Jensen, Jette
Have, Christian T
Izarzugaza, Jose MG
Belling, Kirstine
availability:
available
types:
sequence
description:
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.
accessURL: https://doi.org/10.5524/100173
storedIn:
GigaScience Database
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
GigaDB
homePage: http://gigadb.org/
ID:
SCR:006565
name:
Giga Science Database

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