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Monday, January 25 • 3:40pm - 4:00pm
Comparison of Bioinformatics Tools For Detection and Identification of Fish Pathogens In Metagenomic Samples

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AUTHORS: Kensey Thurner*, Purdue University

ABSTRACT: The use of next-generation sequencing (NGS) to investigate metagenomic samples is becoming more common due to decreased costs. In response, numerous bioinformatics tools have appeared to deal with the large amount of data being produced. One emerging application of NGS with metagenomic samples (e.g. fish spleen) is the detection and identification of pathogens. NGS has several advantages over traditional assay methods including the ability to detect novel pathogens, no requirement for lethal sampling methods. In this study, we sought to identify the best available bioinformatics tools and pipelines for the detection and identification of pathogenic organisms in metagenomic samples acquired from fish tissue. We analyzed raw read output from Illumina MiSeq produced by whole shotgun sequencing of spleen and plasma samples collected from 24 wild-caught fish to compare emerging bioinformatics tools designed specifically for metagenomics, microbial or viral read data with more traditional, broadly-applicable tools (e.g. ABySS and BLAST). We attempted to characterize variation in total detections, number of false positives, detection by pathogen type (i.e. virus, bacteria, etc.), spleen (high percentage of host DNA) vs plasma (low percentage of host DNA), time required and accessibility.

Monday January 25, 2016 3:40pm - 4:00pm EST