RT Journal Article
SR Electronic
T1 Haplotype-aware variant calling enables high accuracy in nanopore long-reads using deep neural networks
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.03.04.433952
DO 10.1101/2021.03.04.433952
A1 Kishwar Shafin
A1 Trevor Pesout
A1 Pi-Chuan Chang
A1 Maria Nattestad
A1 Alexey Kolesnikov
A1 Sidharth Goel
A1 Gunjan Baid
A1 Jordan M. Eizenga
A1 Karen H. Miga
A1 Paolo Carnevali
A1 Miten Jain
A1 Andrew Carroll
A1 Benedict Paten
YR 2021
UL http://biorxiv.org/content/early/2021/03/05/2021.03.04.433952.abstract
AB Long-read sequencing has the potential to transform variant detection by reaching currently difficult-to-map regions and routinely linking together adjacent variations to enable read based phasing. Third-generation nanopore sequence data has demonstrated a long read length, but current interpretation methods for its novel pore-based signal have unique error profiles, making accurate analysis challenging. Here, we introduce a haplotype-aware variant calling pipeline PEPPER-Margin-DeepVariant that produces state-of-the-art variant calling results with nanopore data. We show that our nanopore-based method outperforms the short-read-based single nucleotide variant identification method at the whole genome-scale and produces high-quality single nucleotide variants in segmental duplications and low-mappability regions where short-read based genotyping fails. We show that our pipeline can provide highly-contiguous phase blocks across the genome with nanopore reads, contiguously spanning between 85% to 92% of annotated genes across six samples. We also extend PEPPER-Margin-DeepVariant to PacBio HiFi data, providing an efficient solution with superior performance than the current WhatsHap-DeepVariant standard. Finally, we demonstrate de novo assembly polishing methods that use nanopore and PacBio HiFi reads to produce diploid assemblies with high accuracy (Q35+ nanopore-polished and Q40+ PacBio-HiFi-polished).Competing Interest StatementThe authors have declared no competing interest.