TY - JOUR
T1 - Repetitive DNA and next-generation sequencing
T2 - Computational challenges and solutions
AU - Treangen, Todd J.
AU - Salzberg, Steven L.
PY - 2012/1
Y1 - 2012/1
N2 - Repetitive DNA sequences are abundant in a broad range of species, from bacteria to mammals, and they cover nearly half of the human genome. Repeats have always presented technical challenges for sequence alignment and assembly programs. Next-generation sequencing projects, with their short read lengths and high data volumes, have made these challenges more difficult. From a computational perspective, repeats create ambiguities in alignment and assembly, which, in turn, can produce biases and errors when interpreting results. Simply ignoring repeats is not an option, as this creates problems of its own and may mean that important biological phenomena are missed. We discuss the computational problems surrounding repeats and describe strategies used by current bioinformatics systems to solve them.
AB - Repetitive DNA sequences are abundant in a broad range of species, from bacteria to mammals, and they cover nearly half of the human genome. Repeats have always presented technical challenges for sequence alignment and assembly programs. Next-generation sequencing projects, with their short read lengths and high data volumes, have made these challenges more difficult. From a computational perspective, repeats create ambiguities in alignment and assembly, which, in turn, can produce biases and errors when interpreting results. Simply ignoring repeats is not an option, as this creates problems of its own and may mean that important biological phenomena are missed. We discuss the computational problems surrounding repeats and describe strategies used by current bioinformatics systems to solve them.
UR - http://www.scopus.com/inward/record.url?scp=83855165105&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=83855165105&partnerID=8YFLogxK
U2 - 10.1038/nrg3117
DO - 10.1038/nrg3117
M3 - Review article
C2 - 22124482
AN - SCOPUS:83855165105
VL - 13
SP - 36
EP - 46
JO - Nature Reviews Genetics
JF - Nature Reviews Genetics
SN - 1471-0056
IS - 1
ER -