<commit_before># This file contains mappings reference genome IDs and species for alignments
# where the former are used as prefixes in Bowtie index file names.
# 
# Each entry in this file corresponds to a mapping of species for a given
# reference genome identifier in the following format
#   key = value
# where the key is the reference genome ID and the value is a list of species
# and synonyms separated by the '|' character. The first value in the species
# list will be used as the primary display name for the aligned reference
# genome.
#
# Note that multiple species may map to a single reference genome, for example
# closely-related species. 
#
Ath.TAIR7 = Arabidopsis thaliana (thale cress) | arabidopsis_thaliana | arabidopsis thaliana | a thaliana | thale cress
bacteria.NCBI = Bacteria (~2000 genomes)
Cel.WS200 = Caenorhabditis elegans (nematode worm) | caenorhabditis_elegans | caenorhabditis elegans | c elegans | nematode worm | worm
Cfa.BROADD2 = Canis familiaris (dog) | canis_familiaris | canis familiaris | dog
Cja.calJac1 = Callithrix jacchus (marmoset) | callithrix_jacchus | callithrix jacchus | marmoset
Cpo.CavPor3 = Cavia porcellus (guinea pig) | cavia_porcellus | cavia porcellus | guinea pig
Ddi.090731 = Dictyostelium discoideum | dictyostelium_discoideum
Dmg.dm3 = Drosophila melanogaster (fruit fly) | drosophila_melanogaster | drosophila melanogaster | fruit fly
Eco.W3110 = Escherichia coli | e_coli | e coli
fungi.RefSeq = Fungi
Gga.WASHUC2 = Gallus gallus (chicken) | gallus_gallus | gallus gallus | chicken
Ggo.gorGor3 = Gorilla gorilla | gorilla_gorilla | gorilla gorilla | gorilla
Hsa.GRCh37 = Homo sapiens (human) | homo_sapiens | homo sapiens | human
Mdo.BROADO5 = Monodelphis domestica (opossum) | monodelphis_domestica | monodelphis domestica | opossum
Mml.MMUL1 = Macaca mulatta (macaque) | macaca_mulatta | macaca mulatta | macaque
Mmu.NCBIM37 = Mus musculus (mouse) | mus_musculus | mus musculus | mouse | Mus musculus tc1 (trisomy Hsa21 mouse) | mus_musculus_tc1 | Mus musculus (Algerian mouse) | mus_spretus | mus spretus
Ocu.OryCun2 = Oryctolagus cuniculus (rabbit) | oryctolagus_cuniculus | oryctolagus cuniculus | rabbit
Pha.BCM_v1 = Papio hamadryas (baboon) | papio_hamadryas | paio hamadryas | baboon
phix174 = Phi X 174 | phix
Ppy.WU_202 = Pongo pygmaeus (orangutan) | pongo_pygmaeus | orangutan
Ptr.CHIMP2 = Pan troglodytes (chimpanzee) | pan_troglodytes | pan troglodytes | chimpanzee
Rno.RNOR3_4 = Rattus norvegicus (rat) | rattus_norvegicus | rattus norvegicus | rat
Sce.SGD1.01 = Saccharomyces cerevisiae (yeast) | saccharomyces_cerevisiae | saccharomyces cerevisiae | yeast
Tni.TETRAODON8 = Tetraodon nigroviridis (puffer fish) | tetraodon_nigroviridis | tetraodon nigroviridis | puffer fish
viruses.NCBI = Viruses (~1700 genomes)
Xtr.JGI4_1 = Xenopus tropicalis (frog) | xenopus_tropicalis | xenopus tropicalis | Xenopus laevis (frog) | xenopus_laevis | xenopus laevis | frog
Nle.Nleu1 = Nomascus leucogenys (northern white cheeked gibbon) | nomascus_leucogenys | nomascus leucogenys | northern white cheeked gibbon | gibbon<commit_msg>Updated reference genome mappings<commit_after># This file contains mappings reference genome IDs and species for alignments
# where the former are used as prefixes in Bowtie index file names.
# 
# Each entry in this file corresponds to a mapping of species for a given
# reference genome identifier in the following format
#   key = value
# where the key is the reference genome ID and the value is a list of species
# and synonyms separated by the '|' character. The first value in the species
# list will be used as the primary display name for the aligned reference
# genome.
#
# Note that multiple species may map to a single reference genome, for example
# closely-related species. 
#
ath.TAIR10 = Arabidopsis thaliana (thale cress) | arabidopsis_thaliana | arabidopsis thaliana | thale cress
bacteria.NCBI = Bacteria
cel.WBcel235 = Caenorhabditis elegans (roundworm) | caenorhabditis_elegans | caenorhabditis elegans | c elegans
cfa.CanFam3.1 = Canis familiaris (dog) | canis_familiaris | canis familiaris | dog
cjc.C_jacchus3.2.1 = Callithrix jacchus (marmoset) | callithrix_jacchus | callithrix jacchus | marmoset
cpo.cavPor3 = Cavia porcellus (guinea pig) | cavia_porcellus | cavia porcellus | guinea pig
ddi.dictybase.01 = Dictyostelium discoideum (slime mold) | dictyostelium_discoideum | dictyostelium discoideum
dme.BDGP6 = Drosophila melanogaster (fruitfly) | drosophila_melanogaster | drosophila melanogaster | fruitfly | fruit fly
dre.GRCz10 = Danio rerio (zebrafish) | danio_rerio | danio rerio | zebrafish
eco.ASM1024v1 = Escherichia coli | escherichia_coli | e coli
fungi.NCBI = Fungi
gga.Galgal4 = Gallus gallus (chicken) | gallus_gallus | gallus gallus | chicken
ggo.gorGor3.1 = Gorilla gorilla | gorilla_gorilla | gorilla gorilla | gorilla
hsa.hs37d5 = Homo sapiens (human) | homo_sapiens | homo sapiens | human
mcc.MMUL1 = Macaca mulatta (Rhesus macaque) | macaca_mulatta | macaca mulatta | rhesus macaque | macaque
mdo.monDom5 = Monodelphis domestica (opossum) | monodelphis_domestica | monodelphis domestica | opossum
mmu.NCBIM37 = Mus musculus (mouse) | mus_musculus | mus musculus | mouse | mus_spretus | mus spretus
nle.Nleu1 = Nomascus leucogenys (northern white-cheeked gibbon) | nomascus_leucogenys | nomascus leucogenys | gibbon
ocu.OryCun2 = Oryctolagus cuniculus (rabbit) | oryctolagus_cuniculus | oryctolagus cuniculus | rabbit
pan.PapAnu2 = Papio anubis (olive baboon) | papio_anubis | papio anubis | olive baboon | baboon
phix.Illumina.RTA = Phi X 174 | phix
pon.PPYG2 = Pongo abelii (orangutan) | pongo_abelii | pongo abelii | orangutan
ptr.CHIMP2.1.4 = Pan troglodytes (chimpanzee) | pan_troglodytes | pan troglodytes | chimpanzee
ribosomal_RNA = Ribomsomal RNA (human)
rno.Rnor6 = Rattus norvegicus (rat) | rattus_norvegicus | rattus norvegicus | rat
sce.R64-1-1 = Saccharomyces cerevisiae (brewer's yeast) | saccharomyces_cerevisiae | saccharomyces cerevisiae | yeast
tni.TETRAODON8 = Tetraodon nigroviridis (pufferfish) | tetraodon_nigroviridis | tetraodon nigroviridis | pufferfish
viruses.NCBI = Viruses
xtr.JGI_4.2 = Xenopus tropicalis (western clawed frog) | xenopus_tropicalis | xenopus tropicalis | frog
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