MetaSV: an accurate method-aware merging algorithm for structural variations
Marghoob Mohiyuddin,John C. Mu,Jian Li,Narges Bani Asadi,Mark Gerstein,Alexej Abyzov,Wing Hung Wong,Hugo Y. K. Lam +7 more
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This article is published in F1000Research.The article was published on 2014-07-25 and is currently open access. It has received 0 citations till now.read more
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Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads
TL;DR: Pindel, a pattern growth approach, is presented, to detect breakpoints of large deletions and medium-sized insertions from paired-end short reads and to demonstrate the efficiency of the computer program and accuracy of the results.
Journal ArticleDOI
BreakDancer: An algorithm for high resolution mapping of genomic structural variation
Ken Chen,John W. Wallis,Michael D. McLellan,David E. Larson,Joelle Kalicki,Craig Pohl,Sean McGrath,Michael C. Wendl,Qunyuan Zhang,Devin P. Locke,Xiaoqi Shi,Robert S. Fulton,Timothy J. Ley,Richard K. Wilson,Li Ding,Elaine R. Mardis +15 more
TL;DR: The algorithm BreakDancer predicts a wide variety of structural variants including insertion-deletions (indels), inversions and translocations and sensitively and accurately detected indels ranging from 10 base pairs to 1 megabase pair that are difficult to detect via a single conventional approach.
Journal ArticleDOI
CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing
TL;DR: By genotyping CNVs in the CEPH, Yoruba, and Chinese-Japanese populations, it is estimated that at least 11% of all CNV loci involve complex, multi-allelic events, a considerably higher estimate than reported earlier.
Journal ArticleDOI
Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library
Hugo Y. K. Lam,Xinmeng Jasmine Mu,Adrian M. Stütz,Andrea Tanzer,Philip Cayting,Michael Snyder,Michael Snyder,Philip M. Kim,Jan O. Korbel,Mark Gerstein +9 more
TL;DR: A library of breakpoints at nucleotide resolution from collating and standardizing ~2,000 published SVs is assembled, finding that the occurrence of insertions and deletions is more balanced than previously reported and that NAHR-formed breakpoints are associated with relatively rigid, stable DNA helices.
Journal ArticleDOI
TIGRA: A Targeted Iterative Graph Routing Assembler for breakpoint assembly
TL;DR: A targeted iterative graph routing assembler, TIGRA, is developed, which implements a set of novel data analysis routines to achieve effective breakpoint assembly from next-generation sequencing data and was able to accurately assemble the majority of deletion and mobile element insertion breakpoints.