Abstract：
:Long nanopore reads are advantageous in de novo genome assembly. However, nanopore reads usually have broad error distribution and high-error-rate subsequences. Existing error correction tools cannot correct nanopore reads efficiently and effectively. Most methods trim high-error-rate subsequences during error correction, which reduces both the length of the reads and contiguity of the final assembly. Here, we develop an error correction, and de novo assembly tool designed to overcome complex errors in nanopore reads. We propose an adaptive read selection and two-step progressive method to quickly correct nanopore reads to high accuracy. We introduce a two-stage assembler to utilize the full length of nanopore reads. Our tool achieves superior performance in both error correction and de novo assembling nanopore reads. It requires only 8122 hours to assemble a 35X coverage human genome and achieves a 2.47-fold improvement in NG50. Furthermore, our assembly of the human WERI cell line shows an NG50 of 22 Mbp. The high-quality assembly of nanopore reads can significantly reduce false positives in structure variation detection.
journal_name
Nat Communjournal_title
Nature communicationsauthors
Chen Y,Nie F,Xie SQ,Zheng YF,Dai Q,Bray T,Wang YX,Xing JF,Huang ZJ,Wang DP,He LJ,Luo F,Wang JX,Liu YZ,Xiao CLdoi
10.1038/s41467-020-20236-7subject
Has Abstractpub_date
2021-01-04 00:00:00pages
60issue
1issn
2041-1723pii
10.1038/s41467-020-20236-7journal_volume
12pub_type
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