TY - JOUR
T1 - Recovering full-length viral genomes from metagenomes
AU - Smits, Saskia L
AU - Bodewes, Rogier
AU - Ruiz-González, Aritz
AU - Baumgärtner, Wolfgang
AU - Koopmans, Marion P
AU - Osterhaus, Albert D M E
AU - Schürch, Anita C
PY - 2015
Y1 - 2015
N2 - 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.
AB - 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.
U2 - 10.3389/fmicb.2015.01069
DO - 10.3389/fmicb.2015.01069
M3 - Article
C2 - 26483782
SN - 1664-302X
VL - 6
SP - 1069
JO - Frontiers in Microbiology
JF - Frontiers in Microbiology
ER -
