A haplotype-aware de novo assembly of related individuals using pedigree graph

Abstract

Motivation:Reconstructing high-quality haplotype-resolved assemblies for related individuals of various species has important applications in understanding Mendelian diseases along with evolutionary and comparative genomics. Through major genomics sequencing efforts such as the Personal Genome Project, the Vertebrate Genome Project (VGP), the Earth Biogenome Project (EBP) and the Genome in a Bottle project (GIAB), a variety of sequencing datasets from mother-father-child trios of various diploid species are becoming available. Current trio assembly approaches are not designed to incorporate long-read sequencing data from parents in a trio, and therefore require relatively high coverages of costly long-read data to produce high-quality assemblies. Thus, building a trio-aware assembler capable of producing accurate and chromosomal-scale diploid genomes in a pedigree, while being cost-effective in terms of sequencing costs, is a pressing need of the genomics community. Results: We present a novel pedigree-graph-based approach to diploid assembly using accurate Illumina data and long-read Pacific Biosciences (PacBio) data from all related individuals, thereby generalizing our previous work on single individuals. We demonstrate the effectiveness of our pedigree approach on a simulated trio of pseudo-diploid yeast genomes with different heterozygosity rates, and real data from Arabidopsis Thaliana. We show that we require as little as 30× coverage Illumina data and 15× PacBio data from each individual in a trio to generate chromosomal-scale phased assemblies. Additionally, we show that we can detect and phase variants from generated phased assemblies. Availability: https://github.com/shilpagarg/WHdenovo

LongPhase: an ultra-fast chromosome-scale phasing algorithm for small and large variants

“…However, the additional cost of these approaches is too high for population-scale phasing projects. Besides, the sequencing of trios is not always possible, and the trio-based method will lose novel variants in offspring [19,20]. Consequently, the improvement of phasing range for long-read only sequencing is still in high demand for large-scale sequencing projects [21].…”

Recovering individual haplotypes and a contiguous genome assembly from pooled long read sequencing of the diamondback moth (Lepidoptera: Plutellidae)

“…These simple occurrences can be partitioned and subsequently collapsed or phased (2,5,7). Alternatively, pedigree information, such as trios, can be leveraged by either partitioning F1 read data a priori (8,9) or integrating the pedigree information into the assembly graph itself (10). These latter approaches are robust to HDRs, and in organisms with relatively low repeat content, the reconstruction of fully phased diploid chromosomes is eminently achievable.…”

Accurate chromosome-scale haplotype-resolved assembly of human genomes

“…PacBio CCS sequencing for PGP-1. Library Preparation: Genomic DNA was converted into a SMRTbell™ library as previously described 9 but with a few modifications to generate slightly larger inserts. Specifically, genomic DNA was sheared using the MegaruptorR from Diagenode with the 30kb shearing protocol using a long hydropore cartridge.…”