hum0386-v1Release info

Localized assembly for long reads enables genome-wide analysis of repetitive regions at single-base resolution in human genomes

Aims

Long-read sequencing data has a high error rate, and its handling has not been established. Therefore, it is important to establish useful bioinformatics analysis methods. Mapping-based analysis and whole-genome-assembly-based variant detection have problems such as errors due to repetitive sequences and lack of nucleotide sequence information. Compared to deletions, insertions are difficult to analyze because many of them are derived from repetitive sequences and sequence information is difficult to obtain. In this study, we developed a novel analysis method for long reads and applied it to whole genome analysis of two samples to elucidate the entire human insertion sequence and insertion mechanism.

Methods

We sequenced the genomic DNA of NA18943 from a B cell line using a single platform, MinION. The sequencing data totaled 231.6 Gbp (77× coverage).

Participants/materials

NA18943 is a healthy sample used in the HapMap project. We performed whole genome sequencing of NA18943 using Oxford Nanopore sequencer.

URL

N/A

Principal investigator

Akihiro Fujimoto

Affiliation

Graduate School of Medicine,The University of Tokyo