conserved-primer-design

Use when an agent needs to call the VirusPrimerPro Agent API instead of the GUI, or prepare viral genome inputs for it: request/use API keys, download viral genomes from NCBI, install/run MAFFT, check and repair abnormal sequences, prepare phylogenetic trees/annotations, upload aligned FASTA/tree/GenBank files, poll runs, and fetch artifacts.

Use when an agent needs a stricter or publication-grade phylogeny workflow for PhyloGuide, including tree/MSA validation, FastTree/IQ-TREE planning, and external-tree checks.

Use when an agent must define viral genotype, subtype, clade, lineage, target/background groups, or PhyloGuide groups from cited literature before primer or tNGS panel design.

Use when an agent must split tNGS or multiplex primer pairs into pools while minimizing primer-primer interaction risk and reporting pool overflows.

Use when an agent must evaluate primer candidates for wet-lab constraints such as length, GC, Tm, degeneracy, self-complementarity, pair complementarity, and amplicon size.

Use when an agent must select, filter, deduplicate, and document NCBI/GenBank/reference viral genomes before alignment, primer design, PhyloGuide, or tNGS panel design.

Use when an agent must batch-submit, poll, summarize, retry, or compare long-running VirusPrimerPro Agent API jobs without holding a long HTTP connection open.

Use when an agent must screen primer candidates or tNGS panel primers for host, near-neighbor, background, or co-infection off-target binding before reporting or ordering primers.

Use when an agent must turn primer pair candidates into a tiled or multiplex tNGS amplicon panel with target coverage, overlap, selected pairs, and uncovered gap reporting.

Use when an agent must combine taxonomy, accession manifest, specificity, primer QC, and panel reports into a reproducible design release report.

Use when an agent must convert selected and pooled primer pairs into order sheets, pooling plans, and 96-well plate maps for wet-lab handoff.