MetaGraph: Indexing and Analysing Nucleotide Archives at Petabase-scale

The amount of biological sequencing data available in public repositories is growing exponentially, forming an invaluable biomedical research resource. Yet, making all this sequencing data searchable and easily accessible to life science and data science researchers is an unsolved problem. We present MetaGraph, a versatile framework for the scalable analysis of extensive sequence repositories. MetaGraph efficiently indexes vast collections of sequences to enable fast search and comprehensive analysis. A wide range of underlying data structures offer different practically relevant trade-offs between the space taken by the index and its query performance. MetaGraph provides a flexible methodological framework allowing for index construction to be scaled from consumer laptops to distribution onto a cloud compute cluster for processing terabases to petabases of input data. Achieving compression ratios of up to 1,000-fold over the already compressed raw input data, MetaGraph can represent the content of large sequencing archives in the working memory of a single compute server. We demonstrate our framework’s scalability by indexing over 1.4 million whole genome sequencing (WGS) records from NCBI’s Sequence Read Archive, representing a total input of more than three petabases. Besides demonstrating the utility of MetaGraph indexes on key applications, such as experiment discovery, sequence alignment, error correction, and differential assembly, we make a wide range of indexes available as a community resource, including those over 450,000 microbial WGS records, more than 110,000 fungi WGS records, and more than 20,000 whole metagenome sequencing records. A subset of these indexes is made available online for interactive queries. All indexes created from public data comprising in total more than 1 million records are available for download or usage in the cloud. As an example of our indexes’ integrative analysis capabilities, we introduce the concept of differential assembly, which allows for the extraction of sequences present in a foreground set of samples but absent in a given background set. We apply this technique to differentially assemble contigs to identify pathogenic agents transfected via human kidney transplants. In a second example, we indexed more than 20,000 human RNA-Seq records from the TCGA and GTEx cohorts and use them to extract transcriptome features that are hard to characterize using a classical linear reference. We discovered over 200 trans-splicing events in GTEx and found broad evidence for tissue-specific non-A-to-I RNA-editing in GTEx and TCGA.