Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from single-end reads.
CONCLUSIONS
We developed Breakpointer, a fast algorithm to locate breakpoints of structural variants (SVs) from single-end reads produced by next-generation sequencing. By taking advantage of local non-uniform read distribution and misalignments created by SVs, Breakpointer scans the alignment of single-end reads to identify regions containing potential breakpoints. The detection of such breakpoints can indicate insertions longer than the read length and SVs located in repetitve regions which might be missd by other methods. Thus, Breakpointer complements existing methods to locate SVs from single-end reads.


BACKGROUND
https://github.com/ruping/Breakpointer


BACKGROUND
ruping@molgen.mpg.de


BACKGROUND
Supplementary material is available at Bioinformatics online.
Department of Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany. ruping@molgen.mpg.de
Ruping
R
Sun
Michael I
MI
Love
Tomasz
T
Zemojtel
Anne-Katrin
AK
Emde
Ho-Ryun
HR
Chung
Martin
M
Vingron
Stefan A
SA
Haas
D000465:Algorithms; D016477:Artifacts; D019295:Computational Biology / Q000379:methods*; D056914:Genomic Structural Variation; D006801:Humans; D017422:Sequence Analysis, DNA / Q000379:methods*