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Concentration Assay
In Silico
Nanopore Sequencing
Precision long-read metagenomics sequencing for food safety by detection and assembly of Shiga toxin-producing Escherichia coli in irrigation water 
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Enriched irrigation water (Water) was artificially contaminated with 10-fold dilutions of E . coli EDL933_2 (+Ecoli) with a starting concentration of 7 x 10 8 CFU/ml (Water+Ecoli1). Reads were analyzed by the <t>EPI2ME</t> WIMP workflow. Bacterial species contributing more than 1% of the classified reads are shown and the sum of the remaining species identified are included as “Other”.
Precision long-read metagenomics sequencing for food safety by detection and assembly of Shiga toxin-producing Escherichia coli in irrigation water 
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A) Direct comparison of quantitative qPCR detection with de novo assembly limits by nanopore sequencing informs detection and classification of STECs. B) Pipeline for detection and classification of STECs in enriched irrigation water using nanopore sequencing and <t>EPI2ME</t> cloud-based services to identify reads of a desired taxa for de novo assembly with Flye and in silico analysis.
Precision long-read metagenomics sequencing for food safety by detection and assembly of Shiga toxin-producing Escherichia coli in irrigation water PLoS ONE, 2021 Jan 14
"Enriched irrigation water (Water) was artificially contaminated with 10-fold dilutions of E . coli EDL933_2 (+Ecoli) with a starting concentration of 7 x 10 8 CFU/ml (Water+Ecoli1). Reads were analyzed by the <t>EPI2ME</t> WIMP workflow. Bacterial species contributing more than 1% of the classified reads are shown and the sum of the remaining species identified are included as “Other”. "
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