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Register a new userRobust haplotype-resolved assembly of diploid individuals without parental data
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Routine single-sample haplotype-resolved assembly remains an unresolved problem. Here we describe a new algorithm that combines PacBio HiFi reads and Hi-C chromatin interaction data to produce a haplotype-resolved assembly without the sequencing of parents. Applied to human and other vertebrate samples, our algorithm consistently outperforms existing single-sample assembly pipelines and generates assemblies of comparable quality to the best pedigree-based assemblies.
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The accurate prediction of biological features from genomic data is paramount for precision medicine, sustainable agriculture and climate change research. For decades, neural network models have been widely popular in fields like computer vision, astrophysics and targeted marketing given their prediction accuracy and their robust performance under big data settings. Yet neural network models have not made a successful transition into the medical and biological world due to the ubiquitous characteristics of biological data such as modest sample sizes, sparsity, and extreme heterogeneity. Results: Here, we investigate the robustness, generalization potential and prediction accuracy of widely used convolutional neural network and natural language processing models with a variety of heterogeneous genomic datasets. While the perspective of a robust out-of-the-box neural network model is out of reach, we identify certain model characteristics that translate well across datasets and could serve as a baseline model for translational researchers. Here, we investigate the robustness, generalization potential and prediction accuracy of widely used convolutional neural network and natural language processing models with a variety of heterogeneous genomic datasets. While the perspective of a robust out-of-the-box neural network model is out of reach, we identify certain model characteristics that translate well across datasets and could serve as a baseline model for translational researchers.
Background: Haplotypes, the ordered lists of single nucleotide variations that distinguish chromosomal sequences from their homologous pairs, may reveal an individuals susceptibility to hereditary and complex diseases and affect how our bodies respond to therapeutic drugs. Reconstructing haplotypes of an individual from short sequencing reads is an NP-hard problem that becomes even more challenging in the case of polyploids. While increasing lengths of sequencing reads and insert sizes {color{black} helps improve accuracy of reconstruction}, it also exacerbates computational complexity of the haplotype assembly task. This has motivated the pursuit of algorithmic frameworks capable of accurate yet efficient assembly of haplotypes from high-throughput sequencing data. Results: We propose a novel graphical representation of sequencing reads and pose the haplotype assembly problem as an instance of community detection on a spatial random graph. To this end, we construct a graph where each read is a node with an unknown community label associating the read with the haplotype it samples. Haplotype reconstruction can then be thought of as a two-step procedure: first, one recovers the community labels on the nodes (i.e., the reads), and then uses the estimated labels to assemble the haplotypes. Based on this observation, we propose ComHapDet - a novel assembly algorithm for diploid and ployploid haplotypes which allows both bialleleic and multi-allelic variants. Conclusions: Performance of the proposed algorithm is benchmarked on simulated as well as experimental data obtained by sequencing Chromosome $5$ of tetraploid biallelic emph{Solanum-Tuberosum} (Potato). The results demonstrate the efficacy of the proposed method and that it compares favorably with the existing techniques.
Background - The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly. Results - In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies. Conclusions - Many current genome assemblers produced useful assemblies, containing a significant representation of their genes, regulatory sequences, and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another.
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We study the problem of robust domain adaptation in the context of unavailable target labels and source data. The considered robustness is against adversarial perturbations. This paper aims at answering the question of finding the right strategy to make the target model robust and accurate in the setting of unsupervised domain adaptation without source data. The major findings of this paper are: (i) robust source models can be transferred robustly to the target; (ii) robust domain adaptation can greatly benefit from non-robust pseudo-labels and the pair-wise contrastive loss. The proposed method of using non-robust pseudo-labels performs surprisingly well on both clean and adversarial samples, for the task of image classification. We show a consistent performance improvement of over $10%$ in accuracy against the tested baselines on four benchmark datasets.
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