CBI Reference Genomes

References

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

Plant References

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

Building References

Scripts for building reference genomes. See build_xx.sh

Directory Structure

`References/`

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:

`References/[Species]/[Source]/[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.

`Archive/`

Contains the original files used to build reference genomes, including iGenome archives and gzipped FASTA files.

`scripts/`

Utility scripts used for building reference genomes.

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