Challenges in the analysis of viral metagenomes

Rose, Rebecca; Constantinides, Bede; Tapinos, Avraam; Robertson, David L; Prosperi, Mattia

Coverage: The number of times a genome (or part thereof) has been sequenced. de Bruijn graph: A network of nodes and edges, where each edge represents a k-mer found in the collection of reads, and each node represents either the prefix or suffix of the k-mer. De novo assembly: Reconstruction of short sequences into longer sequences (or contigs), without use of a reference sequence Digital signal processing data transformation: Analytical techniques for transforming sequential data into a domain representative of data features. Discrete Fourier transform: A spectral analysis technique for identifying sine and cosine frequency components in numerical signal data. Discrete wavelet transform: A spectral analysis technique for decomposing data to its frequency and spatial components. k-mer: A subsequence of length k. Many genomic analyses involve decomposition of sequences into all possible subsequences of a specified length k. Numerical sequence representation: Numerical mapping of nucleotide sequences, permitting the application of signal processing transformation approaches.