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Workflow of the HUBDesign pipeline

Probe design for simultaneous, targeted capture of diverse metagenomic targets

HUBDesign: A bioinformatic pipeline for designing probes capable of capturing broad targets of interest in metagenomic settings.

Sep 16, 2021

Authors: Zachery W. Dickson, Dirk Hackenberger, Melanie Kuch, Art Marzok, Arinjay Banerjee, Laura Rossi, Jennifer AnnKlowak, Alison Fox-Robichaud, Karen Mossmann, Matthew S.Miller, Michael G.Surette, Geoffrey Brian Golding, Hendrik Poinar

Cell Reports Methods, September 2021. DOI:


The compounding challenges of low signal, high background, and uncertain targets plague many metagenomic sequencing efforts. One solution has been DNA capture, wherein probes are designed to hybridize with target sequences, enriching them in relation to their background. However, balancing probe depth with breadth of capture is challenging for diverse targets. To find this balance, we have developed the HUBDesign pipeline, which makes use of sequence homology to design probes at multiple taxonomic levels. This creates an efficient probe set capable of simultaneously and specifically capturing known and related sequences. We validated HUBDesign by generating probe sets targeting the breadth of coronavirus diversity, as well as a suite of bacterial pathogens often underlying sepsis. In separate experiments demonstrating significant, simultaneous enrichment, we captured SARS-CoV-2 and HCoV-NL63 in a human RNA background and seven bacterial strains in human blood. HUBDesign ( has broad applicability wherever there are multiple organisms of interest.

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