These high error rates in corrected nanopore reads can introduce misassemblies. Moreover, the average identity of reads corrected by Canu is only 92%, which is far less accurate than that of corrected PacBio SMRT reads. For example, correcting 30X coverage human nanopore reads using the error correction tool in Canu requires 29 K central process unit (CPU) hours 19. Error correction tools in current assemblers were originally designed for PacBio SMRT (Single Molecule, Real-time) reads and cannot efficiently correct nanopore reads. However, errors in nanopore reads are more complex than those in PacBio reads 20, 21 (see “Results”). The recently released R9 flow cell from Oxford Nanopore technology can generate reads that are up to 1 M in length and with read N50 > 100 kb, which may significantly improve the contiguity of assembly 5, 6, 7, 19. On the other hand, the “correction then assembly” approach can provide highly continuous and accurate genome assemblies 9, 10, 11. However, directly assembling the genome using error-prone SMS reads can increase assembly errors in the genome sequence, which affects the quality of reference genome and results in bias in downstream analysis, especially in complicated genome regions 10, 18. Due to the high computational cost of error correction, the “correction then assembly” approach is usually slower than the “assembly then correction” approach. Conversely, assemblers, such as miniasm 12, Flye 13, wtdbg2 14, Shasta 15, Smartdenovo 16, and Raven 17, assemble the genome using error-prone reads and then correct the assembled genome. The two strategies currently used for de novo genome assembly from SMS reads are “correction then assembly” and “assembly then correction.” Assemblers, such as Falcon 9, Canu 10, and MECAT 11, first correct SMS reads and then assemble the genome using corrected reads.
However, SMS reads usually have high error rates 8. Single-molecule sequencing (SMS) technologies, developed by Pacific Bioscience and Oxford Nanopore, yield long reads that can significantly increase the number of solvable repetitive genome regions and improve the contiguity of assembly 4, 5, 6, 7. Reconstructing the genome sequence of a species or individual in a population is one of the most important tasks in genomics 1, 2, 3. The high-quality assembly of nanopore reads can significantly reduce false positives in structure variation detection. Furthermore, our assembly of the human WERI cell line shows an NG50 of 22 Mbp.
It requires only 8122 hours to assemble a 35X coverage human genome and achieves a 2.47-fold improvement in NG50. Our tool achieves superior performance in both error correction and de novo assembling nanopore reads.
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We introduce a two-stage assembler to utilize the full length of nanopore reads. We propose an adaptive read selection and two-step progressive method to quickly correct nanopore reads to high accuracy. Here, we develop an error correction, and de novo assembly tool designed to overcome complex errors in nanopore reads. Most methods trim high-error-rate subsequences during error correction, which reduces both the length of the reads and contiguity of the final assembly. Existing error correction tools cannot correct nanopore reads efficiently and effectively. However, nanopore reads usually have broad error distribution and high-error-rate subsequences.
Long nanopore reads are advantageous in de novo genome assembly.
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