🧬 eDNA metabarcoding primer sets

eDNA metabarcoding primer sets with target gene, organism group, primer sequences, and expected amplicon size (insert, excluding primers). Use the Genome Browser tab to visualise in-silico PCR results against reference mitochondrial, chloroplast, and nuclear rDNA sequences.

About

This tool visualises the binding positions of eDNA metabarcoding primer sets on reference genomes using in-silico PCR. To report issues or suggest primers to add, reach out to @PieterPrvst.

Methodology

In-silico PCR is performed using fuzzy string matching with a tolerance of up to 4 substitutions per primer, allowing for degenerate bases and minor mismatches. IUPAC ambiguity codes in primer sequences are expanded to character classes before matching. Primer pairs producing an amplicon larger than 3× the published insert size are excluded as likely false positives. Amplicon sizes shown are insert sizes (excluding primers), consistent with published values.

Reference genomes

Sequences are fetched from NCBI GenBank. Gene annotations are parsed from GenBank feature tables; tRNA features are included for chloroplast genomes only.