TY - JOUR
T1 - A Guide to Sequencing for Long Repetitive Regions
AU - Kono, Nobuaki
N1 - Publisher Copyright:
© 2023. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.
PY - 2023
Y1 - 2023
N2 - Full-length analysis of genes with highly repetitive sequences is challenging in two respects: assembly algorithm and sequencing accuracy. The de Bruijn graph often used in short-read assembly cannot distinguish adjacent repeat units. On the other hand, the accuracy of long reads is not yet high enough to identify each and every repeat unit. In this chapter, I present an example of a strategy to solve these problems and obtain the full length of long repeats by combining the extraction and assembly of repeat units based on overlap-layout-consensus and scaffolding by long reads.
AB - Full-length analysis of genes with highly repetitive sequences is challenging in two respects: assembly algorithm and sequencing accuracy. The de Bruijn graph often used in short-read assembly cannot distinguish adjacent repeat units. On the other hand, the accuracy of long reads is not yet high enough to identify each and every repeat unit. In this chapter, I present an example of a strategy to solve these problems and obtain the full length of long repeats by combining the extraction and assembly of repeat units based on overlap-layout-consensus and scaffolding by long reads.
KW - De novo sequencing
KW - Highly repetitive sequence
KW - Non-model organism
KW - Overlap-layout-consensus
KW - Structural protein
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U2 - 10.1007/978-1-0716-2996-3_10
DO - 10.1007/978-1-0716-2996-3_10
M3 - Article
C2 - 36781726
AN - SCOPUS:85147952981
SN - 1064-3745
VL - 2632
SP - 131
EP - 146
JO - Methods in molecular biology (Clifton, N.J.)
JF - Methods in molecular biology (Clifton, N.J.)
ER -