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Abstract MotivationIntegrative analysis of large-scale single-cell data collected from diverse cell populations promises an improved understanding of complex biological systems. While several algorithms have been developed for single-cell RNA-sequencing data integration, many lack the scalability to handle large numbers of datasets and/or millions of cells due to their memory and run time requirements. The few tools that can handle large data do so by reducing the computational burden through strategies such as subsampling of the data or selecting a reference dataset to improve computational efficiency and scalability. Such shortcuts, however, hamper the accuracy of downstream analyses, especially those requiring quantitative gene expression information. ResultsWe present SCEMENT, a SCalablE and Memory-Efficient iNTegration method, to overcome these limitations. Our new parallel algorithm builds upon and extends the linear regression model previously applied in ComBat to an unsupervised sparse matrix setting to enable accurate integration of diverse and large collections of single-cell RNA-sequencing data. Using tens to hundreds of real single-cell RNA-seq datasets, we show that SCEMENT outperforms ComBat as well as FastIntegration and Scanorama in runtime (upto 214× faster) and memory usage (upto 17.5× less). It not only performs batch correction and integration of millions of cells in under 25 min, but also facilitates the discovery of new rare cell types and more robust reconstruction of gene regulatory networks with full quantitative gene expression information. Availability and implementationSource code freely available for download at https://github.com/AluruLab/scement, implemented in C++ and supported on Linux. 

Abstract MotivationGene network reconstruction from gene expression profiles is a compute- and data-intensive problem. Numerous methods based on diverse approaches including mutual information, random forests, Bayesian networks, correlation measures, as well as their transforms and filters such as data processing inequality, have been proposed. However, an effective gene network reconstruction method that performs well in all three aspects of computational efficiency, data size scalability, and output quality remains elusive. Simple techniques such as Pearson correlation are fast to compute but ignore indirect interactions, while more robust methods such as Bayesian networks are prohibitively time consuming to apply to tens of thousands of genes. ResultsWe developed maximum capacity path (MCP) score, a novel maximum-capacity-path-based metric to quantify the relative strengths of direct and indirect gene–gene interactions. We further present MCPNet, an efficient, parallelized gene network reconstruction software based on MCP score, to reverse engineer networks in unsupervised and ensemble manners. Using synthetic and real Saccharomyces cervisiae datasets as well as real Arabidopsis thaliana datasets, we demonstrate that MCPNet produces better quality networks as measured by AUPRC, is significantly faster than all other gene network reconstruction software, and also scales well to tens of thousands of genes and hundreds of CPU cores. Thus, MCPNet represents a new gene network reconstruction tool that simultaneously achieves quality, performance, and scalability requirements. Availability and implementationSource code freely available for download at https://doi.org/10.5281/zenodo.6499747 and https://github.com/AluruLab/MCPNet, implemented in C++ and supported on Linux. 

Abstract Motivation Variation graph representations are projected to either replace or supplement conventional single genome references due to their ability to capture population genetic diversity and reduce reference bias. Vast catalogues of genetic variants for many species now exist, and it is natural to ask which among these are crucial to circumvent reference bias during read mapping. Results In this work, we propose a novel mathematical framework for variant selection, by casting it in terms of minimizing variation graph size subject to preserving paths of length α with at most δ differences. This framework leads to a rich set of problems based on the types of variants [e.g. single nucleotide polymorphisms (SNPs), indels or structural variants (SVs)], and whether the goal is to minimize the number of positions at which variants are listed or to minimize the total number of variants listed. We classify the computational complexity of these problems and provide efficient algorithms along with their software implementation when feasible. We empirically evaluate the magnitude of graph reduction achieved in human chromosome variation graphs using multiple α and δ parameter values corresponding to short and long-read resequencing characteristics. When our algorithm is run with parameter settings amenable to long-read mapping (α = 10 kbp, δ = 1000), 99.99% SNPs and 73% SVs can be safely excluded from human chromosome 1 variation graph. The graph size reduction can benefit downstream pan-genome analysis. Availability and implementation https://github.com/AT-CG/VF. Supplementary information Supplementary data are available at Bioinformatics online.