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SECEDO: SNV-based subclone detection using ultra-low coverage single-cell DNA sequencing
(2021)bioRxivRecently developed single-cell DNA sequencing technologies enable whole-genome, amplification-free sequencing of thousands of cells at the cost of ultra-low coverage of the sequenced data (< 0.05x per cell), which mostly limits their usage to the identification of copy number alterations (CNAs) in multi-megabase segments. Aside from CNA-based subclone detection, single-nucleotide variant (SNV)-based subclone detection may contribute ...Working Paper -
Using Genome Graph Topology to Guide Annotation Matrix Sparsification
(2020)bioRxivSince the amount of published biological sequencing data is growing exponentially, efficient methods for storing and indexing this data are more needed than ever to truly benefit from this invaluable resource for biomedical research. Labeled de Bruijn graphs are a frequently-used approach for representing large sets of sequencing data. While significant progress has been made to succinctly represent the graph itself, efficient methods for ...Working Paper -
MetaGraph: Indexing and Analysing Nucleotide Archives at Petabase-scale
(2020)bioRxivThe 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 ...Working Paper