A haplotype-awarede novoassembly of related individuals using pedigree sequence graph

Abstract

Motivation Reconstructing high-quality haplotype-resolved assemblies for related individuals has important applications in Mendelian diseases and population genomics. Through major genomics sequencing efforts such as the Personal Genome Project, the Vertebrate Genome Project (VGP) and the Genome in a Bottle project (GIAB), a variety of sequencing datasets from trios of diploid genomes are becoming available. Current trio assembly approaches are not designed to incorporate long- and short-read data from mother–father–child trios, 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 of all individuals 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 sequence 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 human chromosome. 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 and implementation https://github.com/shilpagarg/WHdenovo.

Advances and opportunities in malaria population genomics

“…The separate assembly of maternal and paternal haplotypes into distinct haplotigs can occur when divergence between similar assembly fragments is mistakenly inferred to represent paralogy (duplication) rather than heterozygosity and if not recognized can inflate the size of a haploid reference assembly. However, haplotype-aware graph-based assembly algorithms have improved tolerance of heterozygosity and are being applied to new anopheline assembly projects 69 , 70 . Further, the DNA input requirements for long-read sequencing have become smaller in recent years, enabling long-read sequencing libraries to be made from a single mosquito instead of a pool of mosquitoes, reducing genetic variation in the sequencing template 71 .…”

Chromosome-scale, haplotype-resolved assembly of human genomes

“…It is possible to switch to a noisy read assembler and to add Illumina data for SNP calling, but assembly accuracy may be reduced due to the elevated sequencing error rate. Second, starting with an unphased assembly, we may miss highly heterozygous regions involving long SVs, as demonstrated in our previous works on small genomes 5,8 . A potential solution is to retain heterozygous events in the initial assembly graph and to scaffold and dissect these events later to generate a phased assembly.…”

“…FALCON-Phase 6 , which extends FALCON-Unzip, uses Hi-C to connect phased sequence blocks and can generate longer haplotypes, but it cannot achieve chromosome-long phasing. Trio binning 7,8 is the only published method that can do this, plus the assembly and phasing of entire chromosomes. It uses sequence reads from both parents to partition the offspring's long reads and then assemble each partition separately.…”

Ratatosk: hybrid error correction of long reads enables accurate variant calling and assembly

“…Yet, centromeres play an important role in cancer genomics [8] while short tandem repeat (STR) expansions associate with a number of genetic diseases [9]. LRS technologies have also enabled de novo haplotype-resolved assemblies with very few contig breaks [10,11]. Finally, LRS technologies overcome chemistry limitations of SRS, in particular GC bias [12] and PCR amplification artifacts [13] causing uneven coverages for reads produced by Illumina platforms.…”