Genome assemblies
Genie's genome catalog is generated from the WashU Epigenome Browser's genome list. It contains 60 assemblies in 31 species groups. The genome picker offers the 57 assemblies in 30 species groups that the eg3 browser engine can draw. The genome is chosen when you create a project and cannot be changed afterwards; see Projects and genomes.
Assemblies by species group
The picker shows one card per species group, in this order. Search in the picker matches species names and assembly ids.
| Species group | Assemblies offered in the picker |
|---|---|
| Human | hg38, hg19, t2t-chm13-v2.0, t2t-chm13-v1.1 |
| Chimp | panTro6, panTro5, panTro4 |
| Gorilla | gorGor4, gorGor3 |
| Gibbon | nomLeu3 |
| Baboon | papAnu2 |
| Rhesus | rheMac10, rheMac8, rheMac3, rheMac2 |
| Marmoset | calJac4, calJac3 |
| Cow | bosTau8 |
| Sheep | oviAri4 |
| Pig | susScr11, susScr3 |
| Rabbit | oryCun2 |
| Dog | canFam6, canFam3, canFam2 |
| Mouse | mm39, mm10, mm9 |
| Rat | rn7, rn6, rn4 |
| Opossum | monDom5 |
| Chicken | GRCg7w, GRCg7b, galGal6, galGal5 |
| Frog | xenTro10 |
| Zebrafish | danRer11, danRer10, danRer7 |
| Spotted Gar | lepOcu1 |
| P. hawaiensis | phaw5 |
| Fruit fly | dm6 |
| C.elegans | ce11 |
| Arabidopsis | araTha1 |
| Brapa | b_chiifu_v3 |
| Seahare | aplCal3 |
| Yeast | sacCer3 |
| P. falciparum | Pfal3D7 |
| Green algae | Creinhardtii5.6 |
| Virus | SARS-CoV-2, MERS, SARS, Ebola, hpv16 |
| Trypanosome | TbruceiTREU927, TbruceiLister427 |
That is 30 species groups and 57 assemblies.
Catalog assemblies not offered in the picker
Three catalog assemblies have no genome definition in the eg3 engine, so the picker leaves them out. A project using one of them could not be drawn.
| Assembly | Species group | Note |
|---|---|---|
bosTau9 | Cow | bosTau8 is offered instead |
rn5 | Rat | rn7, rn6 and rn4 are offered |
GCF_012559485.2 | Crab-eating macaque | The only assembly in its group, so the whole group is left out |
What the assistant sees
The assistant's genome_list_assemblies tool reads the full catalog, so it returns all 60 assemblies, including the three that the picker does not offer. A project's genome is set when the project is created, not by the assistant. See Tools.
Human defaults
Default region
For both hg38 and hg19, a new project opens on the HOXA locus:
chr7:27,053,396-27,373,765
The catalog stores this region as the locus string chr7:27053396-27373765, and the browser header shows the same string for a new project.
Default tracks
| Genome | Default tracks, in order |
|---|---|
hg38 | Ruler, refGene, gencodeV47, MANE selection v1.4, RepeatMasker |
hg19 | Ruler, refGene, gencodeV47, RepeatMasker |
The gene tracks (refGene, gencodeV47, MANE selection v1.4) are drawn from the WashU gene-annotation service. RepeatMasker is read from a bigBed file on vizhub.wustl.edu. In hg19 projects, Genie sets the maxRows option of refGene and gencodeV47 to 10 unless you have set it yourself; in hg38 projects it removes a maxRows value of 10 from refGene, gencodeV47 and MANE selection v1.4 so the engine's default applies.
SARS-CoV-2 defaults
SARS-CoV-2 projects open on the whole genome (NC_045512.2, 29,903 bp) with these tracks:
- Ruler
- NCBI genes
- S protein annotations
- Sequence Diversity (Shannon Entropy)
- Viral RNA expression (nanopore)
- Putative SARS Immune Epitopes
- Omicron: B.1.1.529 and BA lineages
- Transcription regulatory sequences (TRSs)
- Protein_domains
Public data hubs per genome
The Public Data Hubs sheet lists the hubs defined for the project's genome. Only eight assemblies have any:
| Genome | Hubs | Collections include |
|---|---|---|
SARS-CoV-2 | 58 | UniProt protein annotation, CRISPR screens, variants of interest and concern, diagnostics, immune epitopes, recombination events, RNA modifications and expression, sequence variation, Nextstrain, GISAID, NCBI |
hg19 | 23 | ENCODE, Roadmap Epigenomics, IHEC, long-range chromatin interactions, Hi-C from Juicebox and HiGlass, TCGA 450K and 27K arrays, 3D structures, image collection |
hg38 | 14 | ENCODE, Roadmap Epigenomics, IHEC, 4D Nucleome, HPRC long-read methylation, Hi-C from HiGlass, SARS-CoV-2 host responses, image collection |
mm10 | 10 | ENCODE, 4D Nucleome, TaRGET, IHEC, Hi-C from HiGlass, 3D structures, image collection |
Pfal3D7 | 2 | Noble lab, 3D structures |
galGal5 | 1 | 4D Nucleome |
dm6 | 1 | 4D Nucleome |
sacCer3 | 1 | 3D structures |
All other assemblies have no public hubs; you can still add tracks with Remote Tracks.
All offered assemblies
Default region (as the browser header shows it for a new project), default tracks and public hub count for every assembly in the picker. Track names are as they appear in the catalog.
| Assembly | Species group | Default region | Default tracks | Hubs |
|---|---|---|---|---|
hg38 | Human | chr7:27,053,396-27,373,765 | Ruler, refGene, gencodeV47, MANE selection v1.4, RepeatMasker | 14 |
hg19 | Human | chr7:27,053,396-27,373,765 | Ruler, refGene, gencodeV47, RepeatMasker | 23 |
t2t-chm13-v2.0 | Human | chr7:27,088,682-27,155,782 | Ruler, gencodeV35, RepeatMaskerV2 | 0 |
t2t-chm13-v1.1 | Human | chr7:27,203,152-27,363,337 | Ruler, genes from CAT and Liftoff, RepeatMaskerV2 | 0 |
panTro6 | Chimp | chr7:27,270,737-27,274,218 | Ruler, refGene, RepeatMasker | 0 |
panTro5 | Chimp | chr6:52,003,275-52,425,961 | refGene, Ruler, RepeatMasker | 0 |
panTro4 | Chimp | chr6:52,425,275-52,425,961 | Ruler, refGenes, ensembl genes, RepeatMasker | 0 |
gorGor4 | Gorilla | chr6:52,425,275-52,425,961 | Ruler, RepeatMasker | 0 |
gorGor3 | Gorilla | chr6:52,341,785-52,427,411 | Ruler, ensembl genes, RepeatMasker | 0 |
nomLeu3 | Gibbon | chr6:52,425,275-52,425,961 | Ruler, ensembl genes, RepeatMasker | 0 |
papAnu2 | Baboon | chr6:52,425,275-52,425,961 | Ruler, ensembl genes, RepeatMasker | 0 |
rheMac10 | Rhesus | chr3:87,946,310-88,004,460 | Ruler, RefSeq genes, NCBI genes, RepeatMasker | 0 |
rheMac8 | Rhesus | chr16:41,269,988-41,277,524 | refGene, Ruler, RepeatMasker | 0 |
rheMac3 | Rhesus | chr16:34,702,808-34,709,639 | Ruler, refGenes, RepeatMasker | 0 |
rheMac2 | Rhesus | chr1:4,702,808-4,709,639 | Ruler, refGene, RepeatMasker | 0 |
calJac4 | Marmoset | chr8:28,982,643-29,067,973 | Ruler, NCBI genes, RepeatMasker | 0 |
calJac3 | Marmoset | chr6:52,425,275-52,425,961 | Ruler, ncbi Genes, ensembl genes, RepeatMasker | 0 |
bosTau8 | Cow | chr4:69,394,239-69,396,207 | refGene, Ruler, RepeatMasker | 0 |
oviAri4 | Sheep | chr4:68,723,080-68,936,580 | Ruler, RefSeq genes, NCBI genes, RepeatMasker | 0 |
susScr11 | Pig | chr18:45,354,080-45,448,655 | Ruler, RefSeq genes, NCBI genes, RepeatMasker | 0 |
susScr3 | Pig | chr18:50,045,451-50,083,338 | Ruler, RefSeq genes, NCBI genes, RepeatMasker | 0 |
oryCun2 | Rabbit | chr16:34,702,808-34,709,639 | Ruler, refGene, RepeatMasker | 0 |
canFam6 | Dog | chr1:34,702,808-34,709,639 | Ruler, NCBI genes | 0 |
canFam3 | Dog | chr1:34,702,808-34,709,639 | Ruler, refGene, RepeatMasker | 0 |
canFam2 | Dog | chr1:34,702,808-34,709,639 | Ruler, refGene, RepeatMasker | 0 |
mm39 | Mouse | chr6:52,127,920-52,139,724 | Ruler, refGene, gencodeCompVM28, RepeatMasker | 0 |
mm10 | Mouse | chr6:52,149,464-52,164,219 | Ruler, refGene, gencodeCompVM25, RepeatMasker | 10 |
mm9 | Mouse | chr6:52,115,671-52,119,450 | refGene, Ruler, RepeatMasker | 0 |
rn7 | Rat | chr4:81,250,935-81,263,130 | Ruler, RefSeq genes, NCBI genes, RepeatMasker | 0 |
rn6 | Rat | chr6:52,003,275-52,425,961 | refGene, Ruler, RepeatMasker | 0 |
rn4 | Rat | chr1:34,702,808-34,709,639 | Ruler, refGene, RepeatMasker | 0 |
monDom5 | Opossum | chr1:34,702,808-34,709,639 | Ruler, refGene, RepeatMasker | 0 |
GRCg7w | Chicken | 2:35,209,533-36,156,443 | Ruler, gene | 0 |
GRCg7b | Chicken | 2:35,209,533-36,156,443 | Ruler, gene | 0 |
galGal6 | Chicken | chr2:32,588,989-32,593,005 | refGene, Ruler, RepeatMasker | 0 |
galGal5 | Chicken | chr2:32,665,919-32,669,380 | refGene, Ruler, RepeatMasker | 1 |
xenTro10 | Frog | chr6:42,132,107-42,175,007 | Ruler, refGene, ncbi Genes, RepeatMasker | 0 |
danRer11 | Zebrafish | chr19:18,966,018-19,564,024 | refGene, Ruler, RepeatMasker | 0 |
danRer10 | Zebrafish | chr19:18,966,018-19,564,024 | refGene, Ensembl release 91, Ruler | 0 |
danRer7 | Zebrafish | chr6:52,425,275-52,425,961 | Ruler, RepeatMasker | 0 |
lepOcu1 | Spotted Gar | CM001404.1:52,254,368-52,596,869 | Ruler, Ensembl genes, RepeatMasker | 0 |
phaw5 | P. hawaiensis | phaw_50.000135b:538,530-1,003,670 | Ruler, gene | 0 |
dm6 | Fruit fly | chr2L:826,000-851,000 | refGene, Ruler, RepeatMasker | 1 |
ce11 | C.elegans | chrII:14,646,375-14,667,875 | refGene, Ruler, RepeatMasker | 0 |
araTha1 | Arabidopsis | chr1:1,187,813-1,197,077 | TAIR10 genes, Ruler | 0 |
b_chiifu_v3 | Brapa | A01:1,187,813-1,197,077 | Ruler, Brapa genes | 0 |
aplCal3 | Seahare | NW_004797271.1:1,373,952-1,413,093 | Ruler, ncbiGene, RepeatMasker | 0 |
sacCer3 | Yeast | chrII:235,243-243,590 | sgdGene, Ruler | 1 |
Pfal3D7 | P. falciparum | chr1:256,703-310,866 | PlasmoDB 9.0 genes, Ruler | 2 |
Creinhardtii5.6 | Green algae | chr1:219,260-260,991 | PhytozomeGene, Ruler | 0 |
SARS-CoV-2 | Virus | NC_045512.2:1-29,903 | Ruler, NCBI genes, S protein annotations, Sequence Diversity (Shannon Entropy), Viral RNA expression (nanopore), Putative SARS Immune Epitopes, Omicron: B.1.1.529 and BA lineages, Transcription regulatory sequences (TRSs), Protein_domains | 58 |
MERS | Virus | NC_019843.3:1-30,119 | NCBI genes, Ruler, GC Percentage, Sequence Diversity (Shannon Entropy), Mutation Alert | 0 |
SARS | Virus | NC_004718.3:1-29,751 | NCBI genes, Ruler, GC Percentage, Sequence Diversity (Shannon Entropy), Mutation Alert | 0 |
Ebola | Virus | KM034562.1:1-18,957 | NCBI genes, Ruler, GC Percentage, Sequence Diversity (Shannon Entropy), Mutation Alert | 0 |
hpv16 | Virus | NC_001526.4:1-7,906 | NCBI genes, Ruler | 0 |
TbruceiTREU927 | Trypanosome | Tb927_01_v5.1:1-7,906 | TriTrypDB genes, Ruler | 0 |
TbruceiLister427 | Trypanosome | Chr1_3A_Tb427v10:1-7,906 | TriTrypDB genes, Ruler | 0 |
Things the browser does not show
The eg3 genome navigator is turned off in Genie, so no assembly shows a chromosome ideogram, cytoband track or overview minimap, and there is no reference sequence track by default.