Comparison of different assembly and annotation tools on analysis of simulated viral metagenomic communities in the gut.

ABSTRACT:

Background

The main limitations in the analysis of viral metagenomes are perhaps the high genetic variability and the lack of information in extant databases. To address these issues, several bioinformatic tools have been specifically designed or adapted for metagenomics by improving read assembly and creating more sensitive methods for homology detection. This study compares the performance of different available assemblers and taxonomic annotation software using simulated viral-metagenomic data.

Results

We simulated two 454 viral metagenomes using genomes from NCBI's RefSeq database based on the list of actual viruses found in previously published metagenomes. Three different assembly strategies, spanning six assemblers, were tested for performance: overlap-layout-consensu

SUBMITTER: Vazquez-Castellanos JF 

PROVIDER: S-EPMC3901335 | biostudies-literature | 2014 Jan

REPOSITORIES: biostudies-literature