Abstract
Infectious disease metagenomics is driven by the question: "what is causing the disease'?" in contrast to classical metagenome studies which are guided by "what is out there'?" In case of a novel virus, a first step to eventually establishing etiology can be to recover a full-length viral genome from a metagenomic sample. However, retrieval of a full-length genome of a divergent virus is technically challenging and can be time-consuming and costly. Here we discuss different assembly and fragment linkage strategies such as iterative assembly, motif searches, k-mer frequency profiling, coverage profile binning, and other strategies used to recover genomes of potential viral pathogens in a timely and cost-effective manner.
Original language | Undefined/Unknown |
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Journal | Frontiers in Microbiology |
Volume | 6 |
DOIs | |
Publication status | Published - 2015 |
Research programs
- EMC MM-04-27-01