Loading…
NEW THIS YEAR! The schedule of technical sessions is in Sched.org which allows you to search within the schedule, filter the schedule to show sessions only occurring on a certain date, within a track, or in a room. You can also build your own schedule by creating a free account in Sched.org. Click here to return to the main Midwest Fish & Wildlife Conference website. 

PLEASE NOTE: The schedule posted here is as of 1/25/16, and is subject to change. Please check back for updates.

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

Sign up or log in to save this to your schedule and see who's attending!

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
Atrium

Attendees (11)