Species | Source | Build | Contigs | TopHat | HiSat | Notes |
---|---|---|---|---|---|---|
Homo sapiens | UCSC | hg19 | 25 | ✓ | ✓ | iGenomes |
hg38 | 195 | ✓ | ✓ | Includes unlocalized (random) and unplaced (chrUn) contigs, plus EBV. iGenomes | ||
hg38full | 456 | ✓ | ✓ | hg38 (above) plus alternate haplotypes (261 sequences) | ||
HISAT2 | hg19 | 93 | ✓ | Pre-built by CCB | ||
HISAT2 | hg38 | 455 | ✓ | Pre-built by CCB | ||
Mus musculus | Ensembl | GRCm38 | 22 | ✓ | ✓ | iGenomes |
Ceratotherium simum (white rhino) | UCSC | cerSim1 | 3087 |
Species | Name | Plant Type | Source | Build | Contigs |
---|---|---|---|---|---|
Aegilops_tauschii | Tausch's goatgrass | Grass | Gramene | ASM34733v1 | 429892 |
Amborella_trichopoda | Understory shrub | Shrubs/Trees | Gramene | AMTR1.0 | 5745 |
Arabidopsis_lyrata | Lyrate Rock Cress | Flowering | Gramene | v.1.0 | 695 |
Arabidopsis_thaliana | Thale Cress | Flowering | Gramene | TAIR10 | 7 |
Beta_vulgaris | Beet | Herbaceous | Gramene | RefBeet-1.2.2 | 40245 |
Brachypodium_distachyon | Purple False Brome | Grass | Gramene | v1.0 | 83 |
Brassica_napus | Rapeseeds | Flowering | Gramene | AST_PRJEB5043_v1 | 20899 |
Brassica_oleracea | Wild Cabbage | Vegetable | Gramene | v2.1 | 32928 |
Brassica_rapa | Field Mustard | Herbaceous | Gramene | IVFCAASv1 | 40367 |
Chlamydomonas_reinhardtii | Green Algae | Algae | Gramene | v3.1 | 1558 |
Chondrus_crispus | Red Algae/Carageen | Algae | Gramene | ASM35022v2 | 926 |
Corchorus_capsularis | White Jute | Shrubs | Gramene | CCACVL1_1.0 | 16522 |
Cyanidioschyzon_merolae | Red Algae | Algae | Gramene | ASM9120v1 | 22 |
Galdieria_sulphuraria | Red Algae | Algae | Gramene | ASM34128v1 | 433 |
Glycine_max | Soybean | Bean | Gramene | V1.0 | 1168 |
Hordeum_vulgare | Barley | Grass | Gramene | Hv_IBSC_PGSB_v2 | 9 |
Leersia_perrieri | Rice | Grass | Gramene | Lperr_V1.4 | 12 |
Medicago_truncatula | Barrel Clover | Legume | Gramene | MedtrA17_4.0 | 2186 |
Musa_acuminata | Banana | Fruit | Gramene | MA1 | 12 |
Oryza_barthii | African Wild Rice | Grass/Rice | Gramene | O.barthii_v1 | 12 |
Oryza_brachyantha | Wild Rice | Grass/Rice | Gramene | Oryza_brachyantha.v1.4b | 7485 |
Oryza_glaberrima | African Rice | Grass/Rice | Gramene | AGI1.1 | 1951 |
Oryza_glumaepatula | S. American Wild Rice | Grass/Rice | Gramene | ALNU02000000 | 12 |
Oryza_indica | Asian Rice (Indian) | Grass/Rice | Gramene | ASM465v1 | 10490 |
Oryza_longistaminata | Long-Staminate Rice | Grass/Rice | Gramene | O_longistaminata_v1.0 | 60198 |
Oryza_meridionalis | Australian Wild Rice | Grass/Rice | Gramene | Oryza_meridionalis_v1.3 | 12 |
Oryza_nivara | Wild Rice (Indian) | Grass/Rice | Gramene | AWHD00000000 | 12 |
Oryza_punctata | Red Rice (African) | Grass/Rice | Gramene | AVCL00000000 | 12 |
Oryza_rufipogon | Brown Beard Rice | Grass/Rice | Gramene | OR_W1943 | 12 |
Oryza_sativa | Cultivated rice | Grass/Rice | Gramene | IRGSP-1.0 | 61 |
Ostreococcus_lucimarinus | Green Algae | Algae | Gramene | ASM9206v1 | 21 |
Physcomitrella_patens | Earthmoss | Moss | Gramene | ASM242v1 | 2106 |
Populus_trichocarpa | Black Cottonwood | Tree | Gramene | JGI2.0 | 2518 |
Prunus_persica | Peach | Fruit | Gramene | Prupe1_0 | 202 |
Selaginella_moellendorffii | Spikemoss | Lycophyte | Gramene | v1.0 | 759 |
Setaria_italica | Foxtail Millet | Grass | Gramene | JGIv2.0 | 336 |
Solanum_lycopersicum | Tomato | Fruit | Gramene | SL2.50 | 3144 |
Solanum_tuberosum | Potato | Vegetable | Gramene | SolTub_3.0 | 13 |
Sorghum_bicolor | Broom-corn | Grass | Gramene | Sorghum_bicolor_v2 | 1535 |
Theobroma_cacao | Cacao tree | Tree | Gramene | Theobroma_cacao_20110822 | 711 |
Trifolium_pratense | Red Clover | Flowering | Gramene | Trpr | 8595 |
Triticum_aestivum | Common Wheat | Grass | Gramene | TGACv1 | 735945 |
Triticum_urartu | Red Wild Einkorn | Grass | Gramene | ASM34745v1 | 499222 |
Vitis_vinifera | Common Grape | Fruiting | Gramene | IGGP_12x | 33 |
Zea_mays | Maize/Corn | Vegetable | Gramene | AGPv4 | 267 |
Scripts for building reference genomes. See build_xx.sh
This directory contains the reference genome sequences, indexes, and annotations. The contents of this directory are kept in sync with /lustre/groups/cbi/shared/References
using the rsync_lustre.py
script.
The following directory structure is used for each build:
For example, Human reference genome with UCSC annotations, build hg19 is located at References/Homo_sapiens/UCSC/hg19
.
Within each build directory there are two optional subdirectories:
Sequence/
: contains sequence data (FASTA) and sequence indexes, including BLAST, Bowtie, Hisat2, etc.Annotation/
: contains annotation data including SNVs, genes, Tophat2Index.
Contains the original files used to build reference genomes, including iGenome archives and gzipped FASTA files.
Utility scripts used for building reference genomes.