dcdanko / macrobial-genomes Goto Github PK

common macrobial genomes, downloaded from various sources

house cat, felCat8.fa.gz, Nov. 2014 (ICGSC Felis_catus_8.0/felCat8) assembly of the cat genome, 'http://hgdownload.cse.ucsc.edu/goldenPath/felCat8/bigZips/' cow, bosTau8.fa.gz, Dec. 2009 (UMD_3.1.1/bosTau8) assembly of the cow genome (bosTau8, University of Maryland Bos_taurus_UMD_3.1.1), 'http://hgdownload.cse.ucsc.edu/goldenPath/bosTau8/bigZips/' pig, susScr11.fa.gz, Feb. 2017 (Sscrofa11.1/susScr11) assembly of the pig genome (susScr11, The Swine Genome Sequencing Consortium (SGSC)), 'http://hgdownload.cse.ucsc.edu/goldenPath/susScr11/bigZips/' chicken, galGal5.fa.gz, Dec 2015 (Gallus_gallus-5.0/galGal5) assembly of the chicken genome (galGal5, International Chicken Genome Consortium), 'http://hgdownload.cse.ucsc.edu/goldenPath/galGal5/bigZips/' rat, rn6.fa.gz, Jul. 2014 (RGSC 6.0/rn6) assembly of the rat genome (rn6, RGSC Rnor_6.0), 'http://hgdownload.cse.ucsc.edu/goldenPath/rn6/bigZips/' rabbit, oryCun2.fa.gz, Apr. 2009 (Broad/oryCun2) assembly of the rabbit genome (oryCun2, Broad Institute oryCun2 (NCBI project 12819, AAGW00000000)), 'http://hgdownload.cse.ucsc.edu/goldenPath/oryCun2/bigZips/' squirrel, speTri2.fa.gz, Nov. 2011 (Broad/speTri2) assembly of the squirrel genome (speTri2, Broad Institute (GCA_000236235.1)), 'http://hgdownload.cse.ucsc.edu/goldenPath/speTri2/bigZips/' zebrafish, danRer11.fa.gz, May 2017 (GRCz11/danRer11) assembly of the zebrafish genome (danRer11, Genome Reference Consortium), 'http://hgdownload.cse.ucsc.edu/goldenPath/danRer11/bigZips/' housefly, dm6.fa.gz, Aug. 2014 (BDGP Release 6 + ISO1 MT/dm6) assembly of the D. melanogaster genome (dm6, The FlyBase Consortium/Berkeley Drosophila Genome Project/Celera Genomics), 'http://hgdownload.cse.ucsc.edu/goldenPath/dm6/bigZips/' tilapia, oreNil2.fa.gz, Jan. 2011 (Nile tilapia/oreNil2) assembly of the nile tilapia genome (oreNil2, Broad Institute of MIT and Harvard Orenil1.1 (GCA_000188235.1)), 'http://hgdownload.cse.ucsc.edu/goldenPath/oreNil2/bigZips/' canFam3.fa.gz, Sep 2011 GCA_000002285.2, 'http://genome.ucsc.edu/cgi-bin/hgGateway?db=canFam3' mouse, mm10.fa.gz, Dec. 2011 (GRCm38/mm10) assembly of the mouse genome (mm10, Genome Reference Consortium Mouse Build 38 (GCA_000001635.2)), 'http://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/' maize, Zea_mays.AGPv3.22.dna_sm.genome.fa.gz, B73 RefGen_v3 2013, 'https://maizegdb.org/genome/genome_assembly/B73%20RefGen_v3' apple, Malus_x_domestica.v3.0.a1_contigs.fasta.gz, Malus x domestica Whole Genome v3.0.a1 2015, 'https://www.rosaceae.org/species/malus/malus_x_domestica/genome_v3.0.a1' orange, Cclementina_182_v1.softmasked.fa, Citrus clementina genome v1.0 (JGI) 2012, 'https://www.citrusgenomedb.org/analysis/156' honeybee, GCF_000002195.4_Amel_4.5_genomic.fna.gz, 4.5 2011, 'https://www.ncbi.nlm.nih.gov/assembly/GCF_000002195.4/' pigeon, GCF_000337935.1_Cliv_1.0_genomic.fna.gz, Columba livia 1.0, 'https://www.ncbi.nlm.nih.gov/genome/10719' horse, equCab2.fa.gz, Sep. 2007 assembly of the horse genome (equCab2, Broad Institute EquCab2), 'http://hgdownload.soe.ucsc.edu/goldenPath/equCab2/bigZips/' lettuce, GCA_002870075.1_Lsat_Salinas_v7_genomic.fna.gz, v7, 'https://www.ncbi.nlm.nih.gov/genome/352' guinea-pig, cavPor3.fa.gz, Feb. 2008 assembly of the guinea pig genome (cavPor3, Broad Institute cavPor3), 'http://hgdownload.cse.ucsc.edu/goldenPath/cavPor3/bigZips/' hedgehog, eriEur2.fa,gz, May 2012 (EriEur2.0/eriEur2) assembly of the hedgehog genome (eriEur2, Broad Institute EriEur2.0), 'http://hgdownload.cse.ucsc.edu/goldenPath/eriEur2/bigZips/' painted-turtle, chrPic1.fa.gz, Dec. 2011 (v3.0.1/chrPic1) assembly of the painted turtle genome, 'http://hgdownload.cse.ucsc.edu/goldenPath/chrPic1/bigZips/' potato, PGSC_DM_v3_scaffolds.fasta.gz, S. tuberosum Group Phureja DM1-3 Version 3 DM scaffold sequences, 'http://solanaceae.plantbiology.msu.edu/pgsc_download.shtml' tomato, S_lycopersicum_chromosomes.3.00.fa.gz, build 3.0, 'https://solgenomics.net/organism/Solanum_lycopersicum/genome' strawberry, fvesca_v1.1_scaffolds.fna.gz, Fragaria vesca Whole Genome v1.1, 'https://www.rosaceae.org/species/fragaria/fragaria_vesca/genome_v1.1' bannana, musa_acuminata_v2_pseudochromosome.fna.gz, Musa acuminata DH Pahang v2 (released January 2016), 'http://banana-genome-hub.southgreen.fr/download' grape, grape.fna.gz, , 'http://www.genoscope.cns.fr/externe/GenomeBrowser/Vitis/'