The following table lists species for which reference files have been built or are in development using the BuildIndices pipeline. For more detailed information about each species and the links to the reference fies, please see the BuildIndices pipeline page.
| Species |
Latin Name |
Genomic Reference |
Gene Annotation File |
Status |
| Human |
Homo sapiens |
GRCh38, primary assembly (PRI) |
GENCODE Release 43 GRCh38.p13 |
Production |
| Mouse |
Mus musculus |
mm39, primary assembly (PRI) |
GENCODE Release M32 GRCm39 |
Production |
| Macaque |
Macaca mulatta |
mmul10 |
RefSeq annotation version 103 |
Production |
| Marmoset |
Callithrix jacchus |
mCalJa1.2.pat.X (GenBank Accession GCA_011100555.2 and RefSeq Accession GCF_011100555.1) |
Custom GTF with mitochondrial chromosomes |
Production |
| Armadillo (Nine-banded) |
Dasypus novemcinctus |
mDasNov1.hap2 (NCBI) |
RefSeq GCF_030445035.1-RS_2023_07 |
Available |
| Ferret |
Mustela putorius furo |
ASM1176430v1.1 (NCBI) |
GCF_011764305.1 (NCBI) |
Available |
| Mouse lemur |
Microcebus murinus |
Mmur_3.0 (NCBI) |
GCF_000165445.2 (NCBI) |
Available |
| Naked mole rat |
Heterocephalus glaber |
HetGla_female_1.0 (NCBI) |
GCF_000247695.1 (NCBI) |
Available |
| Opossum |
Monodelphis domestica |
mMonDom1.pri (NCBI) |
RefSeq GCF_027887165.1-RS_2023_05 |
Available |
| Owl monkey |
Aotus nancymaae |
86718_ANA_hifiasm-v0.15.2.pri (NCBI) |
GCF_030222135.1 (NCBI) |
Available |
| Pig |
Sus scrofa |
Sscrofa11.1 (NCBI) |
NCBI Annotation Release 106 (RefSeq GCF_000003025.6_Sscrofa11.1) |
Available |
| Rat |
Rattus norvegicus |
mRatBN7.2 (NCBI) |
RefSeq GCF_015227675.2-RS_2023_06 |
Available |
| Treeshrew |
Tupaia belangeri |
TupChi_1.0 (NCBI) |
GCF_000334495.1 (NCBI) |
Coming Soon |
| Chimpanzee |
Pan troglodytes |
NHGRI_mPanTro3-v2.0_pri (NCBI) |
GCF_028858775.2 (NCBI) |
Available |