Ardep, a Rapid Degenerate Primer Design Pipeline Based on k-mers for Amplicon Microbiome Studies

The survey of microbial diversity in various environments has relied upon the widespread use of well-evaluated amplification primers for taxonomic marker genes (e.g., prokaryotic 16S and fungal ITS). However, it is urgent to develop a fast and accurate bioinformatic program to design primers for microbial functional genes to explore more mechanisms in the microbial community. Here, we provide a rapid degenerate primer design pipeline (ARDEP) based on the k -mer algorithm, which can bypass the time-consuming step of sequence alignment to greatly reduce run times while ensuring accuracy. In addition, we developed an open-access platform for the implementation of primer design projects that could also calculate the amplification product length, GC content, Annealing Temperature (Tm), and ΔG of primer self-folding, and identify covered species and functional groups. Using this new platform, we designed primers for several functional genes in the nitrogen cycle, including napA and amoA . Our newly designed primers achieved higher coverage than the commonly used primers for all tested genes. The program and the associated platform that applied the k -mer algorithm could greatly enhance the design and evaluation of primers for environmental microbiome studies

Amplicon · Biology · Computational biology · Gene · Metagenomics · Microbiome · Pipeline (software · Polymerase chain reaction · Primer (cosmetics · Programming language · Bioinformatics and Genomic Networks · Chemistry · Computer Science · Genomics and Phylogenetic Studies · Microbial Community Ecology and Physiology · Genetics

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  Open Access•R C Edgar•Nucleic Acids Research•2004

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