Testing the advantages and disadvantages of short- and long- read eukaryotic metagenomics using simulated reads.

ABSTRACT:

Background

The first step in understanding ecological community diversity and dynamics is quantifying community membership. An increasingly common method for doing so is through metagenomics. Because of the rapidly increasing popularity of this approach, a large number of computational tools and pipelines are available for analysing metagenomic data. However, the majority of these tools have been designed and benchmarked using highly accurate short read data (i.e. Illumina), with few studies benchmarking classification accuracy for long error-prone reads (PacBio or Oxford Nanopore). In addition, few tools have been benchmarked for non-microbial communities.

Results

Here we compare simulated long reads from Oxford Nanopore and Pacific Biosciences (PacBio) with high accuracy I

SUBMITTER: Pearman WS 

PROVIDER: S-EPMC7257156 | biostudies-literature | 2020 May

REPOSITORIES: biostudies-literature