Probe design for simultaneous, targeted capture of diverse metagenomic targets.
Cell Rep Methods
; 1(6): 100069, 2021 Oct 25.
Article
in English
| MEDLINE | ID: covidwho-1763677
ABSTRACT
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 (https//github.com/zacherydickson/HUBDesign) has broad applicability wherever there are multiple organisms of interest.
Full text:
Available
Collection:
International databases
Database:
MEDLINE
Type of study:
Prognostic study
Language:
English
Journal:
Cell Rep Methods
Year:
2021
Document Type:
Article
Affiliation country:
J.crmeth.2021.100069
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