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csiro-crop-informatics / repset

Reproducible evaluation of short read mappers
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Additional genomes for evaluation #36

Closed rsuchecki closed 4 years ago

rsuchecki commented 5 years ago

Can be selected in many ways, this may be a start:

mysql -u anonymous -h mysql-eg-publicsql.ebi.ac.uk -P 4157
use ensemblgenomes_info_41;

Then

SELECT species, assembly_name, assembly_level, base_count \
FROM genome WHERE division = "EnsemblMetazoa" AND assembly_level = "chromosome";
species assembly_name assembly_level base_count
aedes_aegypti AaegL3 chromosome 1383974186
anopheles_darlingi AdarC3 chromosome 136950925
anopheles_gambiae AgamP4 chromosome 273109044
atta_cephalotes Attacep1.0 chromosome 317690795
belgica_antarctica ASM77530v1 chromosome 89583723
caenorhabditis_elegans WBcel235 chromosome 100286401
caenorhabditis_briggsae CB4 chromosome 108384165
culex_quinquefasciatus CpipJ2 chromosome 579057705
drosophila_simulans ASM75419v3 chromosome 124963774
drosophila_pseudoobscura Dpse_3.0 chromosome 152696192
drosophila_yakuba dyak_caf1 chromosome 165693946
drosophila_melanogaster BDGP6 chromosome 143725995
melitaea_cinxia MelCinx1.0 chromosome 389907520
mnemiopsis_leidyi MneLei_Aug2011 chromosome 155875873
nasonia_vitripennis Nvit_2.1 chromosome 295780872
pediculus_humanus PhumU2 chromosome 110804242
sarcoptes_scabiei SscaA1 chromosome 56262437
schistosoma_mansoni ASM23792v2 chromosome 364541798
solenopsis_invicta Si_gnG chromosome 396024718
trichinella_spiralis Tspiralis1 chromosome 63525422

Similarly 

SELECT species, assembly_name, assembly_level, base_count \
FROM genome WHERE division = "EnsemblPlants" AND assembly_level = "chromosome";
species assembly_name base_count
arabidopsis_lyrata v.1.0 206667935
aegilops_tauschii ASM34733v1 3313764331
arabidopsis_thaliana TAIR10 119667750
beta_vulgaris RefBeet-1.2.2 566181630
brachypodium_distachyon Brachypodium_distachyon_v3.0 271163419
brassica_rapa Brapa_1.0 283822783
brassica_oleracea BOL 488622507
chondrus_crispus ASM35022v2 104980420
chlamydomonas_reinhardtii Chlamydomonas_reinhardtii_v5.5 111098438
cyanidioschyzon_merolae ASM9120v1 16728945
dioscorea_rotundata TDr96_F1_Pseudo_Chromosome_v1.0 456674974
cucumis_sativus ASM407v2 193829320
daucus_carota ASM162521v1 421502825
gossypium_raimondii Graimondii2_0 761405269
helianthus_annuus HanXRQr1.0 3027844945
glycine_max Glycine_max_v2.0 978416860
hordeum_vulgare IBSC v2 4834432680
leersia_perrieri Lperr_V1.4 266687832
lupinus_angustifolius LupAngTanjil_v1.0 609203021
manihot_esculenta Manihot esculenta v6 582117524
medicago_truncatula MedtrA17_4.0 412800391
musa_acuminata ASM31385v1 472960417
nicotiana_attenuata NIATTr2 2365682703
ostreococcus_lucimarinus ASM9206v1 13204888
oryza_glaberrima Oryza_glaberrima_V1 316419574
oryza_barthii O.barthii_v1 308272304
oryza_brachyantha Oryza_brachyantha.v1.4b 260838168
oryza_meridionalis Oryza_meridionalis_v1.3 335668232
oryza_glumipatula Oryza_glumaepatula_v1.5 372860283
oryza_punctata Oryza_punctata_v1.2 393816603
oryza_rufipogon OR_W1943 338040714
oryza_nivara Oryza_nivara_v1.0 337950324
oryza_indica ASM465v1 427004890
oryza_sativa IRGSP-1.0 375049285
phaseolus_vulgaris PhaVulg1_0 521076696
physcomitrella_patens Phypa V3 471852792
prunus_persica Prunus_persica_NCBIv2 227411381
populus_trichocarpa Pop_tri_v3 434132815
setaria_italica Setaria_italica_v2.0 405732883
solanum_tuberosum SolTub_3.0 810654046
sorghum_bicolor Sorghum_bicolor_NCBIv3 708735318
solanum_lycopersicum SL2.50 823630941
theobroma_cacao Theobroma_cacao_20110822 345993675
trifolium_pratense Trpr 304842038
triticum_dicoccoides WEWSeq v.1.0 10079039394
triticum_aestivum IWGSC 14547261565
triticum_urartu ASM34745v1 3747163292
vigna_angularis Vigan1.1 466744453
vitis_vinifera 12X 486265422
vigna_radiata Vradiata_ver6 463085359
zea_mays B73 RefGen_v4 2135083061
rsuchecki commented 4 years ago

We have 4 representative in a default run, more can be easily added as needed.