2023 Early Hearing Detection & Intervention Conference
March 5-7, 2023 • Cincinnati, OH
5/22/2018 | 12:15 PM - 12:30 PM | UNDERSTANDING VARIATION ASSOCIATED WITH BIOINFORMATICS PROCESSING OF ENVIRONMENTAL GENOMIC DATA | 420 B
UNDERSTANDING VARIATION ASSOCIATED WITH BIOINFORMATICS PROCESSING OF ENVIRONMENTAL GENOMIC DATA
Metabarcoding is increasingly used in biomonitoring worldwide. The lack of standardized bioinformatics approaches for environmental metabarcoding data compromises data quality. Understanding the sources of variability in the bioinformatics process will help practitioners make informed decisions about where standardization is important and account for uncertainty associated with the bioinformatics process. This study examined variation among a diverse group of bioinformatics workflows through intercalibration. By quantifying the relative contribution of variance at each step of the bioinformatics process, we documented how bioinformatics pipelines influence the ecological interpretation of environmental metabarcoding assessments. Five participating labs each received the same 18S rRNA sequence dataset to analyze through their pipelines. We compared output between labs at sequence counts, OTUs or sequence-types, community composition, taxonomic ID and ecological relationships. Initial analyses resulted in substantial interlaboratory variability in sequence numbers, OTUs and number of families. We reduced variability among labs by reconciling several key steps in the bioinformatic process. The intercalibration process allowed us to develop recommendations that will reduce the overall uncertainty associated with application of metabarcoding for environmental assessment while still allowing flexibility in the bioinformatic process.
- Assessment
- Biological Criteria
- Metagenomics
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Presenters/Authors
Eric Stein
(), Southern California Coastal Water Research Project, erics@sccwrp.org;
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Joshua Steele
(), Southern California Coastal Water Research Project, joshuas@sccwrp.org;
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Anthony Chariton
(), Macquarie University, Anthony.Chariton@mq.edu.au;
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Paul Greenfield
(), Macquarie University, Paul.Greenfield@csiro.au;
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Luke Thompson
(), NOAA Southwest Fisheries Science Center, luke.thompson@noaa.gov;
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John Martinson
(), U.S Environmental Protection Agency, martinson.john@epa.gov;
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Donald Baird
(), Environment and Climate Change Canada @ Canadian Rivers Institute, Department of Biology, University of New Brunswick, Fredericton, NB, Canada, djbaird@unb.ca;
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Erik Pilgrim
(), U.S Environmental Protection Agency, pilgrim.erik@epa.gov;
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Mehrdad Hajibabaei
(), Centre for Biodiversity Genomics & Department of Integrative Biology, University of Guelph, ON, Canada, mhajibab@uoguelph.ca;
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