What species are available for each pipeline?

Common name

Scientific name

Source

Link

Sponge

Amphimedon queenslandica

Ensembl release 55

http://ftp.ensemblgenomes.org/pub/release-55/metazoa/gtf/amphimedon_queenslandica/

Arabidopsis

Arabidopsis halleri

Ensembl release 55

http://ftp.ensemblgenomes.org/pub/release-55/plants/gtf/arabidopsis_halleri/

Arabidopsis Thale cress

Arabidopsis thaliana

Ensembl release 55

http://ftp.ensemblgenomes.org/pub/release-55/plants/gtf/arabidopsis_thaliana/

Bartonella

Bartonella Henselae

Ensembl release 55

https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacteria/release-55/gtf/bacteria_0_collection/bartonella_henselae_str_houston_1_gca_000046705/

Drummond’s Rockcress

Boechera stricta

JGI v1.2

https://phytozome-next.jgi.doe.gov/info/Bstricta_v1_2

Cow

Bos taurus

Ensembl release 108

https://ftp.ensembl.org/pub/release-108/gtf/bos_taurus/

Purple False Brome

Brachypodium distachyon

Ensembl release 55

http://ftp.ensemblgenomes.org/pub/release-55/plants/gtf/brachypodium_distachyon/

Nematode Roundworm

Caenorhabditis elegans

Ensembl release 107

https://ftp.ensembl.org/pub/release-107/gtf/caenorhabditis_elegans/

Yeast

Candida albicans

Ensembl release 55

http://ftp.ensemblgenomes.org/pub/release-55/fungi/gtf/candida_albicans/

Dog

Canis lupus familiaris

Ensembl release 107

https://ftp.ensembl.org/pub/release-107/gtf/canis_lupus_familiaris/

Goat

Capra hircus

Ensembl release 108

https://ftp.ensembl.org/pub/release-108/gtf/capra_hircus/

Painted Turtle

Chrysemys picta bellii

Ensembl release 108

https://ftp.ensembl.org/pub/release-108/gtf/chrysemys_picta_bellii/

COVID19

COVID19 (SARS-CoV-2)

Ensembl MN908947.3

http://ftp.ensemblgenomes.org/pub/viruses/gtf/sars_cov_2/

CHO-K1 Cell Line

Cricetulus griseus

Ensembl release 108

https://ftp.ensembl.org/pub/release-108/gtf/cricetulus_griseus_chok1gshd/

Zebrafish

Danio rerio

Ensembl release 108

https://ftp.ensembl.org/pub/release-108/gtf/danio_rerio/

Water flea

Daphnia pulex

NCBI refseq GCF_021134715.1_ASM2113471v1

https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_021134715.1/

Fruit Fly

Drosophila melanogaster

Ensembl release 108

https://ftp.ensembl.org/pub/release-108/gtf/drosophila_melanogaster/

African Oil Palm

Elaeis guineensis

NCBI refseq GCF_000442705.1

https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000442705.1/

Cat

Felis catus

Ensembl release 107

https://ftp.ensembl.org/pub/release-107/gtf/felis_catus/

Fungus

Fusarium oxysporum

Ensembl release 55

http://ftp.ensemblgenomes.org/pub/release-55/fungi/gtf/fusarium_oxysporum/

Chicken

Gallus gallus

Ensembl release 108

https://ftp.ensembl.org/pub/release-108/gtf/gallus_gallus/

Human

Homo sapiens

Ensembl release 107

https://ftp.ensembl.org/pub/release-107/gtf/homo_sapiens/

Barley

Hordeum vulgare - barley

Ensembl release 55

http://ftp.ensemblgenomes.org/pub/release-55/plants/gtf/hordeum_vulgare/

Yeast

Kluyveromyces lactis

NCBI refseq GCF_000002515.2

https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000002515.2/

Mouse

Mus musculus

Ensembl release 107

https://ftp.ensembl.org/pub/release-107/gtf/mus_musculus/

Brain-Eating Amoeba

Naegleria fowleri

NCBI refseq GCF_008403515.1_ASM840351v1

https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_008403515.1/

Starlet Sea Anemone

Nematostella vectensis

NCBI refseq GCF_932526225.1_jaNemVect1.1

https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_932526225.1/

Rabbit

Oryctolagus cuniculus

Ensembl release 108

https://ftp.ensembl.org/pub/release-108/gtf/oryctolagus_cuniculus/

Rice

Oryza sativa

Ensembl release 55

http://ftp.ensemblgenomes.org/pub/release-55/plants/gtf/oryza_sativa/

Western Balsam Poplar Tree

Populus trichocarpa

Ensembl release 55

http://ftp.ensemblgenomes.org/pub/release-55/plants/gtf/populus_trichocarpa/

Pseudomonas

Pseudomonas Aeruginosa

NCBI refseq GCF_000006765.1_ASM676v1.

https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000006765.1/

Rat

Rattus norvegicus

Ensembl release 107

https://ftp.ensembl.org/pub/release-107/gtf/rattus_norvegicus/

Baker’s Yeast

Saccharomyces cerevisiae

Ensembl release 108

https://ftp.ensembl.org/pub/release-108/gtf/saccharomyces_cerevisiae/

Salmon

Salmo salar

Ensembl release 108

https://ftp.ensembl.org/pub/release-108/gtf/salmo_salar/

Tomato

Solanum lycopersicum

Ensembl release 55

http://ftp.ensemblgenomes.org/pub/release-55/plants/gtf/solanum_lycopersicum/

Potato

Solanum tuberosum

Ensembl release 55

http://ftp.ensemblgenomes.org/pub/release-55/plants/gtf/solanum_tuberosum/

Sorghum

Sorghum bicolor

Ensembl release 55

http://ftp.ensemblgenomes.org/pub/release-55/plants/gtf/sorghum_bicolor/

Pig

Sus scrofa

Ensembl release 108

https://ftp.ensembl.org/pub/release-108/gtf/sus_scrofa/

Cacao Tree

Theobroma cacao criollo

Ensembl release 55

http://ftp.ensemblgenomes.org/pub/release-55/plants/gtf/theobroma_cacao_criollo/

Fungus

Yarrowia lipolytica

Ensembl release 55

http://ftp.ensemblgenomes.org/pub/release-55/fungi/gtf/yarrowia_lipolytica/

Maize/Corn

Zea mays

Ensembl release 55

http://ftp.ensemblgenomes.org/pub/release-55/plants/gtf/zea_mays/