Do you cov me? Effect of coverage reduction on metagenome shotgun sequencing studies.

ABSTRACT: Shotgun metagenomics sequencing is a powerful tool for the characterization of complex biological matrices, enabling analysis of prokaryotic and eukaryotic organisms and viruses in a single experiment, with the possibility of reconstructing de novo the whole metagenome or a set of genes of interest. One of the main factors limiting the use of shotgun metagenomics on wide scale projects is the high cost associated with the approach. We set out to determine if it is possible to use shallow shotgun metagenomics to characterize complex biological matrices while reducing costs. We used a staggered mock community to estimate the optimal threshold for species detection. We measured the variation of several summary statistics simulating a decrease in sequencing depth by randomly subsampling

SUBMITTER: Cattonaro F 

PROVIDER: S-EPMC7059852 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature