2023 Early Hearing Detection & Intervention Conference
March 5-7, 2023 • Cincinnati, OH
5/22/2018 | 2:00 PM - 2:15 PM | QIIME: A GOOD BIOINFORMATICS PIPELINE FOR ILLUMINA NEXTSEQ AMPLICION SEQUENCING DATA PROCESSING? | 420 B
QIIME: A GOOD BIOINFORMATICS PIPELINE FOR ILLUMINA NEXTSEQ AMPLICION SEQUENCING DATA PROCESSING?
Quantitative Insights Into Microbial Ecology (QIIME) is one of the most commonly used bioinformatics pipelines for processing data generated from amplicon sequencing, regardless of which next-generation sequencing (NGS) platform is used. Most researchers use NGS and QIIME to characterize microbial communities in different environments; from guts of organisms to soil samples. Although it has been about four years since the Illumina NextSeq was released, there have been fewer publications regarding the use of the NextSeq, especially for downstream bioinformatics processing in comparison to that of other NGS platforms. We constructed a pipeline for downstream bioinformatics processing of data generated from the NextSeq using publically available QIIME scripts. However, instead of looking at microbial communities, we are characterizing fish and invertebrate communities in aquatic ecosystems. In doing so, we are focusing in on using NGS as a tool for early detection and monitoring for Asian Carp. Although the pipeline has been completed, we hope to make this pipeline completely automated with the help of HTCondor.
- Invasive
- Great Lakes
- Genetics
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Presenters/Authors
Yer Lor
(), USGS, ylor@usgs.gov;
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Katie Bockrath
(), USFWS, katherine_bockrath@fws.gov;
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S.Grace McCalla
(), USGS, smccalla@usgs.gov;
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Jon Amberg
(), USGS, jamberg@usgs.gov;
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