Reference genomes
Primer Architect ships a curated set of reference assemblies indexed for off-target screening. Primer design runs on Human (GRCh38), Mouse (GRCm39), E. coli K-12 (U00096.3) and Yeast (R64-1-1); design on the other genomes is coming soon. Off-target checks work on every live genome listed below. All curated genomes are FASTA-stored in gs://tg-primer-architect-genomes and paired with a bowtie2 index used by the off-target check.
Live (12)
These show up in the Off-target analyzer's assembly dropdown and in Step 1 of the design wizard. Genomes marked Designcan continue to primer design; the others are marked “Primer design coming soon” and work in the Off-target analyzer.
| Name | Species | Assembly | Source | ~Size | Use |
|---|---|---|---|---|---|
| Human | Homo sapiens | GRCh38.p14 | GENCODE v48 | 3 GB | Design + off-target |
| Mouse | Mus musculus | GRCm39 | GENCODE M37 | 2.7 GB | Design + off-target |
| Chicken | Gallus gallus | GRCg7b | Ensembl release 113 | 1.1 GB | Off-target |
| Chinese hamster | Cricetulus griseus | CriGri-PICR | Ensembl release 113 | 2.3 GB | Off-target |
| Maize | Zea mays | Zm-B73-REFERENCE-NAM-5.0 | Ensembl Plants release 60 | 2.1 GB | Off-target |
| Pig | Sus scrofa | Sscrofa11.1 | Ensembl release 113 | 2.5 GB | Off-target |
| Zebrafish | Danio rerio | GRCz11 | Ensembl release 113 | 1.4 GB | Off-target |
| Arabidopsis | Arabidopsis thaliana | TAIR10 | Ensembl Plants release 60 | 0.13 GB | Off-target |
| C. elegans | Caenorhabditis elegans | WBcel235 | Ensembl release 113 | 0.1 GB | Off-target |
| Drosophila | Drosophila melanogaster | BDGP6.46 | Ensembl release 113 | 0.15 GB | Off-target |
| Yeast (S. cerevisiae) | Saccharomyces cerevisiae | R64-1-1 | Ensembl release 113 | 0.012 GB | Design + off-target |
| E. coli K-12 | Escherichia coli K-12 MG1655 | U00096.3 | NCBI / GenBank U00096.3 | 0.005 GB | Design + off-target |
Chromosome names in a Custom BED
Custom BED rows use the design genome's coordinates (0-based start, end-exclusive). Human and mouse take UCSC/GENCODE names with or without the chr prefix. E. coli K-12 accepts U00096.3 or its RefSeq twin NC_000913.3. Yeast accepts the Ensembl names (I…XVI, Mito), RefSeq accessions (NC_001133.9…NC_001224.1) or UCSC chrI…chrXVI/chrM. Results show positions in the reference FASTA's own naming. ClinVar/CIViC hotspot avoidance and the Variants tab are human-only.
Coming soon (3)
Tracked in the genome library but not yet indexed end-to-end. These appear in the picker but are disabled.
- Yarrowia lipolytica (Yarrowia lipolytica) —
CLIB 122 - SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) —
MN908947.3 - Influenza A H3N2 (Influenza A virus (H3N2)) —
H3N2 ref panel
Upload your own
Anything off the curated list can be added on demand (for off-target checks — design on uploaded genomes is coming soon). Open the wizard at /design/new, click the genome picker on Step 1, then Upload custom genome at the bottom of the modal. The FASTA streams directly to GCS via a signed URL — multi-gigabyte references work fine — and reappears in the picker tagged yours once indexing finishes (usually under a minute for vertebrate-sized genomes).
Deleting and inspecting your uploaded genomes (including indexing status and any failure messages) happens in the same picker — the trash icon next to each yours row removes the FASTA from storage.
Adding a curated genome
Curated genomes are added in two phases: a FASTA upload to the bucket plus a bowtie2-index Cloud Build (see scripts/index-curated-genomes.sh in the repo). The full end-to-end takes ~30 min per vertebrate-sized assembly and runs on Cloud Build at E2_HIGHCPU_32. Tell us what reference you need and we'll dispatch it.