PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data.
Personal-genomics endeavors, such as the 1000 Genomes project, are generating maps of genomic structural variants by analyzing ends of massively sequenced genome fragments. To process these we developed Paired-End Mapper (PEMer; http://sv.gersteinlab.org/pemer). This comprises an analysis pipeline, compatible with several next-generation sequencing platforms; simulation-based error models, yielding confidence-values for each structural variant; and a back-end database. The simulations demonstrated high structural variant reconstruction efficiency for PEMer's coverage-adjusted multi-cutoff scoring-strategy and showed its relative insensitivity to base-calling errors.
Korbel
Jan O
JO
Gene Expression Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstr, Heidelberg, 69117, Germany. korbel@embl.de
Abyzov
Alexej
A
Mu
Xinmeng Jasmine
XJ
Carriero
Nicholas
N
Cayting
Philip
P
Zhang
Zhengdong
Z
Snyder
Michael
M
Gerstein
Mark B
MB
D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D016678:Genome; D056914:Genomic Structural Variation; D023281:Genomics / Q000379:methods; D020407:Internet; D008957:Models, Genetic; D012984:Software