Natural history bycatch: a pipeline for identifying metagenomic sequences in RADseq data.

ABSTRACT:

Background

Reduced representation genomic datasets are increasingly becoming available from a variety of organisms. These datasets do not target specific genes, and so may contain sequences from parasites and other organisms present in the target tissue sample. In this paper, we demonstrate that (1) RADseq datasets can be used for exploratory analysis of tissue-specific metagenomes, and (2) tissue collections house complete metagenomic communities, which can be investigated and quantified by a variety of techniques.

Methods

We present an exploratory method for mining metagenomic "bycatch" sequences from a range of host tissue types. We use a combination of the pyRAD assembly pipeline, NCBI's blastn software, and custom R scripts to isolate metagenomic sequences from RADseq t

SUBMITTER: Holmes I 

PROVIDER: S-EPMC5907781 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature