A. mellifera (Apr 2011 Amel_4.5/amel5)

NCBI Assembly https://www.ncbi.nlm.nih.gov/assembly/GCF_000002195.4/
NCBI Version Amel_4.5
Source Assembled chromosomes from RefSeq (GCF_000002195.4): ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/195/GCF_000002195.4_Amel_4.5/
UCSC Assembly none
Local Assembly amel5
Bowtie Idx a_mellifera_amel5
liftOver none
RepeatMasker none
MGA FTP ftp://ccg.vital-it.ch/mga/amel5/
UCSC Genome Browser http://genome.ucsc.edu/cgi-bin/hgTracks?genome=amel5&hubUrl=http://epd.vital-it.ch/ucsc/epdHubCustomSpecies/epdHubCustomSpecies.txt
Assembly support status full

A. thaliana (Feb 2011 TAIR10/araTha1)

NCBI Assembly https://www.ncbi.nlm.nih.gov/assembly/GCF_000001735.3/
NCBI Version TAIR10
Source Assembled chromosomes from RefSeq (GCF_000001735.3): ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/735/GCF_000001735.3_TAIR10/
UCSC Assembly araTha1
Local Assembly araTha1
Bowtie Idx a_thaliana_araTha1
liftOver none
RepeatMasker rmsk/rmsk_araTha1.SGA.gz
MGA FTP ftp://ccg.vital-it.ch/mga/araTha1/
UCSC Genome Browser http://genome.ucsc.edu/cgi-bin/hgTracks?genome=araTha1&hubUrl=http://epd.vital-it.ch/ucsc/epdHubCustomSpecies/epdHubCustomSpecies.txt
Assembly support status full

B. taurus (Aug 2006 Btau_3.1/bosTau3)

NCBI Assembly https://www.ncbi.nlm.nih.gov/assembly/GCF_000003205.1/
NCBI Version Btau_3.1
Source Assembled chromosomes from RefSeq (GCF_000003205.1)
UCSC Assembly bosTau3
Local Assembly bosTau3
Bowtie Idx b_taurus_bosTau3
liftOver bosTau3ToHg18, bosTau3ToMm8, bosTau3ToMm9
RepeatMasker rmsk/rmsk_bosTau3.SGA.gz
MGA FTP none
UCSC Genome Browser https://genome.ucsc.edu/cgi-bin/hgTracks?db=bosTau3
Assembly support status partial

B. taurus (Nov 2014 Bos_taurus_UMD_3.1.1/bosTau8)

NCBI Assembly https://www.ncbi.nlm.nih.gov/assembly/GCF_000003055.6/
NCBI Version Bos_taurus_UMD_3.1.1
Source Assembled chromosomes from RefSeq (GCF_000003055.6): ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/003/055/GCF_000003055.6_Bos_taurus_UMD_3.1.1/
UCSC Assembly bosTau8
Local Assembly bosTau8
Bowtie Idx b_taurus_bosTau8
liftOver bosTau8ToHg38, bosTau8ToMm10
RepeatMasker rmsk/rmsk_bosTau8.SGA.gz
MGA FTP none
UCSC Genome Browser https://genome.ucsc.edu/cgi-bin/hgTracks?db=bosTau8
Assembly support status partial

C. familiaris (May 2005 CanFam2.0/canFam2)

NCBI Assembly https://www.ncbi.nlm.nih.gov/assembly/GCF_000002285.2/
NCBI Version CanFam2.0
Source Assembled chromosomes from Refseq (GCF_000002285.2)
UCSC Assembly canFam2
Local Assembly canFam2
Bowtie Idx d_rerio_canFam2
liftOver canFam2ToCanFam3, canFam2ToHg18, canFam2ToHg19, canFam2ToMm9
RepeatMasker rmsk/rmsk_canFam2.SGA.gz
MGA FTP none
UCSC Genome Browser https://genome.ucsc.edu/cgi-bin/hgTracks?db=canFam2
Assembly support status partial

C. familiaris (Sep 2011 CanFam3.1/canFam3)

NCBI Assembly https://www.ncbi.nlm.nih.gov/assembly/GCF_000002285.3/
NCBI Version CanFam3.1
Source Assembled chromosomes from Refseq (GCF_000002285.3): ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/285/GCF_000002285.3_CanFam3.1/
UCSC Assembly canFam3
Local Assembly canFam3
Bowtie Idx d_rerio_canFam3
liftOver canFam3ToCanFam2, canFam3ToHg19, canFam3ToHg38, canFam3ToMm10
RepeatMasker rmsk/rmsk_canFam3.SGA.gz
MGA FTP none
UCSC Genome Browser https://genome.ucsc.edu/cgi-bin/hgTracks?db=canFam3
Assembly support status partial

C. elegans (Oct 2010 WBcel215/ce10)

NCBI Assembly https://www.ncbi.nlm.nih.gov/assembly/GCF_000002985.5/
NCBI Version WBcel215
Source Assembled chromosomes from Genbank (GCA_000002985.2): ftp://ftp.ncbi.nlm.nih.gov/genomes/archive/old_genbank/Eukaryotes/invertebrates/Caenorhabditis_elegans/WBcel215/
UCSC Assembly ce10
Local Assembly ce10
Bowtie Idx c_elegans_ce10
liftOver ce10ToCe4, ce10ToCe6
RepeatMasker rmsk/rmsk_ce10.SGA.gz
MGA FTP ftp://ccg.vital-it.ch/mga/ce10/
UCSC Genome Browser https://genome.ucsc.edu/cgi-bin/hgTracks?db=ce10
Assembly support status full

C. elegans (Feb 2013 WBcel235/ce11)

NCBI Assembly https://www.ncbi.nlm.nih.gov/assembly/GCF_000002985.6/
NCBI Version WBcel235
Source Assembled chromosomes from RefSeq (GCF_000002985.6): ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/985/GCF_000002985.6_WBcel235/
UCSC Assembly ce11
Local Assembly ce11
Bowtie Idx c_elegans_ce11
liftOver ce11ToCe10, ce11ToCe6
RepeatMasker rmsk/rmsk_ce11.SGA.gz
MGA FTP none
UCSC Genome Browser https://genome.ucsc.edu/cgi-bin/hgTracks?db=ce11
Assembly support status partial

C. elegans (Jan 2007 WS170/ce4)

NCBI Assembly none
NCBI Version WS170
Source Assembled chromosomes from RefSeq (suppressed)
UCSC Assembly ce4
Local Assembly ce4
Bowtie Idx c_elegans_ce4
liftOver ce4ToCe6, cer4ToCe10
RepeatMasker rmsk/rmsk_ce4.SGA.gz
MGA FTP none
UCSC Genome Browser https://genome.ucsc.edu/cgi-bin/hgTracks?db=ce4
Assembly support status partial

C. elegans (May 2008 WS190/ce6)

NCBI Assembly https://www.ncbi.nlm.nih.gov/assembly/GCF_000002985.1/
NCBI Version WS190
Source Assembled chromosomes from RefSeq (GCF_000002985.1_WS190): ftp://ftp.ncbi.nih.gov/genomes/refseq/invertebrate/Caenorhabditis_elegans/all_assembly_versions/GCF_000002985.1_WS190/
UCSC Assembly ce6
Local Assembly ce6
Bowtie Idx c_elegans_ce6
liftOver ce6ToCe4, ce6ToCe10
RepeatMasker rmsk/rmsk_ce6.SGA.gz
MGA FTP ftp://ccg.vital-it.ch/mga/ce6/
UCSC Genome Browser https://genome.ucsc.edu/cgi-bin/hgTracks?db=ce6
Assembly support status partial

D. rerio (Sep 2014 GRCz10/danRer10)

NCBI Assembly https://www.ncbi.nlm.nih.gov/assembly/GCF_000002035.5/
NCBI Version GRCz10
Source Assembled chromosomes from Refseq (GCF_000002035.5): ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/035/GCF_000002035.5_GRCz10/
UCSC Assembly danRer10
Local Assembly danRer10
Bowtie Idx d_rerio_danRer10
liftOver danRer10ToHg38, danRer10ToHg19, danRer10ToMm10, danRer10ToDanRer7, danRer10ToRn6
RepeatMasker rmsk/rmsk_danRer10.SGA.gz
MGA FTP none
UCSC Genome Browser https://genome.ucsc.edu/cgi-bin/hgTracks?db=danRer7
Assembly support status partial

D. rerio (July 2010 Zv9/danRer7)

NCBI Assembly https://www.ncbi.nlm.nih.gov/assembly/GCF_000002035.4/
NCBI Version Zv9
Source Assembled chromosomes from Refseq (GCF_000002035.4): ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/035/GCF_000002035.4_Zv9/
UCSC Assembly danRer7
Local Assembly danRer7
Bowtie Idx d_rerio_danRer7
liftOver danRer7ToHg19, danRer7ToMm9, danRer7ToMm10
RepeatMasker rmsk/rmsk_danRer7.SGA.gz
MGA FTP ftp://ccg.vital-it.ch/mga/danRer7/
UCSC Genome Browser https://genome.ucsc.edu/cgi-bin/hgTracks?db=danRer7
Assembly support status full

D. melanogaster (Apr 2006 BDGP R5/dm3)

NCBI Assembly https://www.ncbi.nlm.nih.gov/assembly/GCF_000001215.2/
NCBI Version Release 5 (R5)
Source Assembled chromosomes from Refseq (RELEASE_5): ftp://ftp.ncbi.nih.gov/genomes/archive/old_refseq/Drosophila_melanogaster/RELEASE_5/
UCSC Assembly dm3
Local Assembly dm3
Bowtie Idx d_melanogaster_dm3
liftOver dm3ToDm6
RepeatMasker rmsk/rmsk_dm3.SGA.gz
MGA FTP ftp://ccg.vital-it.ch/mga/dm3/
UCSC Genome Browser https://genome.ucsc.edu/cgi-bin/hgTracks?db=dm3
Assembly support status full

D. melanogaster (Aug 2014 BDGP Rel6 + ISO1 MT/dm6)

NCBI Assembly https://www.ncbi.nlm.nih.gov/assembly/GCF_000001215.4/
NCBI Version Release 6 plus ISO1 MT
Source Assembled chromosomes from Refseq (GCF_000001215.4): ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/215/GCF_000001215.4_Release_6_plus_ISO1_MT
UCSC Assembly dm6
Local Assembly dm6
Bowtie Idx d_melanogaster_dm6
liftOver dm6ToDm3
RepeatMasker rmsk/rmsk_dm6.SGA.gz
MGA FTP ftp://ccg.vital-it.ch/mga/dm6/
UCSC Genome Browser https://genome.ucsc.edu/cgi-bin/hgTracks?db=dm6
Assembly support status full

H. sapiens (March 2006 NCBI36/hg18)

NCBI Assembly https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.12/
NCBI Version NCBI36
Source Assembled chromosomes from RefSeq: ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.2/
UCSC Assembly hg18
Local Assembly hg18
Bowtie Idx h_sapiens_hg18
liftOver hg18ToHg19, hg18ToHg38, hg18ToMm8, hg18ToMm9, hg18ToBosTau3, hg18ToCanFam2, hg18ToPanTro2
RepeatMasker rmsk/rmsk_hg18.SGA.gz
MGA FTP ftp://ccg.vital-it.ch/mga/hg18/
UCSC Genome Browser https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18
Assembly support status full

H. sapiens (Feb 2009 GRCh37/hg19)

NCBI Assembly https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.13/
NCBI Version GRCh37
Source Assembled chromosomes from RefSeq (GCF_000001405.13): ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.37.1/
UCSC Assembly hg19
Local Assembly hg19
Bowtie Idx h_sapiens_hg19
liftOver hg19ToHg18, hg19ToHg38, hg19ToMm9, hg19ToMm10, hg19ToHg19a, hg19ToCanFam2, hg19ToCanFam3, hg19ToDanRer7, hg19ToDanRer10, hg19ToPanTro2, hg19ToRn5, hg19ToRn6, hg19ToSusScr3
RepeatMasker rmsk/rmsk_hg19.SGA.gz
MGA FTP ftp://ccg.vital-it.ch/mga/hg19/
UCSC Genome Browser https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19
Assembly support status full

H. sapiens (Feb 2009 Alternate GRCh37/hg19a)

NCBI Assembly none
NCBI Version none
Source hg19 alternate assembly
UCSC Assembly none
Local Assembly hg19a
Bowtie Idx h_sapiens_hg19a
liftOver hg19aToHg19
RepeatMasker none
MGA FTP none
UCSC Genome Browser none
Assembly support status basic

H. sapiens (Dec 2013 GRCh38/hg38)

NCBI Assembly https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26/
NCBI Version GRCh38
Source Assembled chromosomes from RefSeq (GCF_000001405.26): ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.26_GRCh38/
UCSC Assembly hg38
Local Assembly hg38
Bowtie Idx h_sapiens_hg38
liftOver hg38ToHg19, hg38ToMm10, hg38ToBosTau8, hg38ToCanFam3, hg38ToDanRer10, hg38ToPanTro5, hg38ToRn5, hg38ToRn6, hg38ToSusScr3
RepeatMasker rmsk/rmsk_hg38.SGA.gz
MGA FTP none
UCSC Genome Browser https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19
Assembly support status full

M. musculus (March 2012 GRCm38/mm10)

NCBI Assembly https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.20/
NCBI Version GRCm38
Source Assembled chromosomes from RefSeq (GCF_000001635.20): ftp://ftp.ncbi.nih.gov/genomes/Mus_musculus/ARCHIVE/BUILD.38.1/
UCSC Assembly mm10
Local Assembly mm10
Bowtie Idx m_musculus_mm10
liftOver mm10ToMm9, mm10ToHg19, mm10ToHg38, mm10ToBosTau8, mm10ToCanFam3, mm10ToDanRer10, mm10ToDanRer7, mm10ToOreNil2, mm10ToPanTro5, mm10ToRn5, mm10ToSusScr3
RepeatMasker rmsk/rmsk_mm10.SGA.gz
MGA FTP none
UCSC Genome Browser https://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10
Assembly support status partial

M. musculus (Feb 2006 NCBI36/mm8)

NCBI Assembly https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.15/
NCBI Version NCBI36 (MGSCv36)
Source Assembled chromosomes from RefSeq (GCF_000001635.15): ftp://ftp.ncbi.nih.gov/genomes/Mus_musculus/ARCHIVE/BUILD.36.1/
UCSC Assembly mm8
Local Assembly mm8
Bowtie Idx none
liftOver mm8ToMm9, mm8ToHg18
RepeatMasker rmsk/rmsk_mm8.SGA.gz
MGA FTP none
UCSC Genome Browser https://genome.ucsc.edu/cgi-bin/hgTracks?db=mm8
Assembly support status partial

M. musculus (July 2007 NCBI37/mm9)

NCBI Assembly https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.18/
NCBI Version NCBI37 (MGSCv37)
Source Assembled chromosomes from RefSeq (GCF_000001635.18): ftp://ftp.ncbi.nih.gov/genomes/Mus_musculus/ARCHIVE/BUILD.37.1/
UCSC Assembly mm9
Local Assembly mm9
Bowtie Idx m_musculus_mm9
liftOver mm9ToMm8, mm9ToMm10, mm9ToHg18, mm9ToHg19, mm9ToBosTau3, mm9ToCanFam2, mm9ToDanRer7, mm9ToPanTro2, mm9ToRn5
RepeatMasker rmsk/rmsk_mm9.SGA.gz
MGA FTP ftp://ccg.vital-it.ch/mga/mm9/
UCSC Genome Browser https://genome.ucsc.edu/cgi-bin/hgTracks?db=mm9
Assembly support status full

O. niloticus (Feb 2012 Orenil1.1/oreNil2)

NCBI Assembly https://www.ncbi.nlm.nih.gov/assembly/GCF_000188235.2/
NCBI Version Orenil1.1
Source Assembled chromosomes from Refseq (GCF_000188235.2): ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/188/235/GCF_000188235.2_Orenil1.1/
UCSC Assembly oreNil2
Local Assembly oreNil2
Bowtie Idx o_niloticus_oreNil2
liftOver oreNil2ToMm10
RepeatMasker rmsk/rmsk_oreNil2.SGA.gz
MGA FTP none
UCSC Genome Browser https://genome.ucsc.edu/cgi-bin/hgTracks?db=oreNil2
Assembly support status partial

O. latipes (May 2007 ASM31367v1/oryLat)

NCBI Assembly https://www.ncbi.nlm.nih.gov/assembly/GCF_000313675.1/
NCBI Version ASM276v1
Source Assembled chromosomes from Refseq (GCF_000313675.1): ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/313/675/GCF_000313675.1_ASM31367v1/GCF_000313675.1_ASM31367v1_assembly_structure/
UCSC Assembly none
Local Assembly oryLat
Bowtie Idx o_latipes_oryLat
liftOver none
RepeatMasker none
MGA FTP none
UCSC Genome Browser none
Assembly support status basic

O. sativa Japonica (Oct 2015 IRGSP-1.0/orySatJ)

NCBI Assembly https://www.ncbi.nlm.nih.gov/assembly/GCF_001433935.1/
NCBI Version IRGSP-1.0
Source Assembled chromosomes from Refseq (GCF_001433935.1): ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/433/935/GCF_001433935.1_IRGSP-1.0/
UCSC Assembly none
Local Assembly orySatJ
Bowtie Idx o_sativa_japonica_orySatJ
liftOver none
RepeatMasker none
MGA FTP none
UCSC Genome Browser none
Assembly support status basic

P. troglodytes (Mar 2006 Pan_troglodytes-2.1/panTro2)

NCBI Assembly https://www.ncbi.nlm.nih.gov/assembly/GCF_000001515.3/
NCBI Version Pan_troglodytes-2.1
Source Assembled chromosomes from Refseq (GCF_000001515.3)
UCSC Assembly panTro2
Local Assembly panTro2
Bowtie Idx p_troglodytes_panTro2
liftOver panTro2ToHg18, panTro2ToHg19, panTro2ToMm8, panTro2ToMm9, panTro2ToCanFam2
RepeatMasker rmsk/rmsk_panTro2.SGA.gz
MGA FTP none
UCSC Genome Browser https://genome.ucsc.edu/cgi-bin/hgTracks?db=panTro2
Assembly support status partial

P. troglodytes (May 2016 Pan_tro3.0/panTro5)

NCBI Assembly https://www.ncbi.nlm.nih.gov/assembly/GCF_000001515.7/
NCBI Version Pan_tro3.0
Source Assembled chromosomes from Refseq (GCF_000001515.7): ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/515/GCF_000001515.7_Pan_tro_3.0/GCF_000001515.7_Pan_tro_3.0_assembly_structure/
UCSC Assembly panTro5
Local Assembly panTro5
Bowtie Idx p_troglodytes_panTro5
liftOver panTro5ToHg38, panTro5ToMm10
RepeatMasker rmsk/rmsk_panTro5.SGA.gz
MGA FTP none
UCSC Genome Browser https://genome.ucsc.edu/cgi-bin/hgTracks?db=panTro5
Assembly support status partial

P. falciparum (Oct 2007 ASM276v1/plasFalc1)

NCBI Assembly https://www.ncbi.nlm.nih.gov/assembly/GCF_000002765.1/
NCBI Version ASM276v1
Source Assembled chromosomes from Refseq (GCF_000002765.1)
UCSC Assembly none
Local Assembly plasFalc1
Bowtie Idx p_falciparum_plasFalc1
liftOver none
RepeatMasker none
MGA FTP none
UCSC Genome Browser none
Assembly support status basic

R. norvegicus (Mar 2012 Rnor_5.0/rn5)

NCBI Assembly https://www.ncbi.nlm.nih.gov/assembly/GCF_000001895.4/
NCBI Version Rnor_5.0
Source Assembled chromosomes from RefSeq (GCF_000001895.4): ftp://ftp.ncbi.nlm.nih.gov/genomes/R_norvegicus/ARCHIVE/BUILD.5.1
UCSC Assembly rn5
Local Assembly rn5
Bowtie Idx r_norvegicus_rn5
liftOver rn5ToMm9, rn5ToMm10, rn5ToHg19, rn5ToHg38, rn5ToDanRer7, rn5ToRn6
RepeatMasker rmsk/rmsk_rn5.SGA.gz
MGA FTP none
UCSC Genome Browser https://genome.ucsc.edu/cgi-bin/hgTracks?db=rn5
Assembly support status partial

R. norvegicus (Jul 2014 Rnor_6.0/rn6)

NCBI Assembly https://www.ncbi.nlm.nih.gov/assembly/GCA_000001895.4/
NCBI Version Rnor_6.0
Source Assembled chromosomes from RefSeq (GCF_000001895.4): ftp://ftp.ncbi.nlm.nih.gov/genomes/R_norvegicus/ARCHIVE/BUILD.5.1
UCSC Assembly rn6
Local Assembly rn6
Bowtie Idx r_norvegicus_rn6
liftOver rn6ToRn5, rn6ToHg19, rn6ToHg38, rn6ToDanRer10
RepeatMasker rmsk/rmsk_rn6.SGA.gz
MGA FTP none
UCSC Genome Browser https://genome.ucsc.edu/cgi-bin/hgTracks?db=rn6
Assembly support status partial

S. cerevisiae (June 2008 NCBI2.1/sacCer2)

NCBI Assembly https://www.ncbi.nlm.nih.gov/bioproject/128/
NCBI Version NCBI2.1
Source Assembled chromosomes from RefSeq
UCSC Assembly sacCer2
Local Assembly sacCer2
Bowtie Idx s_cerevisiae_sacCer2
liftOver sacCer2ToSacCer3
RepeatMasker rmsk/rmsk_sacCer2.SGA.gz
MGA FTP none
UCSC Genome Browser https://genome.ucsc.edu/cgi-bin/hgTracks?db=sacCer2
Assembly support status partial

S. cerevisiae (Apr 2011 R64/sacCer3)

NCBI Assembly https://www.ncbi.nlm.nih.gov/assembly/GCF_000146045.2/
NCBI Version R64
Source Assembled chromosomes from RefSeq (GCF_000146045.2): ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/146/045/GCF_000146045.2_R64/
UCSC Assembly sacCer3
Local Assembly sacCer3
Bowtie Idx s_cerevisiae_sacCer3
liftOver sacCer3ToSacCer2
RepeatMasker rmsk/rmsk_sacCer3.SGA.gz
MGA FTP ftp://ccg.vital-it.ch/mga/sacCer3
UCSC Genome Browser https://genome.ucsc.edu/cgi-bin/hgTracks?db=sacCer3
Assembly support status full

S. pombe (Aug 2015 ASM294v2/spo2)

NCBI Assembly https://www.ncbi.nlm.nih.gov/assembly/GCF_000002945.1/
NCBI Version ASM294v2
Source Assembled chromosomes from RefSeq (GCF_000002945.1): ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/945/GCF_000002945.1_ASM294v2/
UCSC Assembly none
Local Assembly spo2
Bowtie Idx s_cerevisiae_sacCer3
liftOver none
RepeatMasker none
MGA FTP ftp://ccg.vital-it.ch/mga/spo2/
UCSC Genome Browser http://genome.ucsc.edu/cgi-bin/hgTracks?genome=spo2&hubUrl=http://epd.vital-it.ch/ucsc/epdHubCustomSpecies/epdHubCustomSpecies.txt
Assembly support status full

S. scrofa (Aug 2011 Sscrofa10.2/susScr3)

NCBI Assembly https://www.ncbi.nlm.nih.gov/assembly/GCF_000003025.5/
NCBI Version Sscrofa10.2
Source Assembled chromosomes from Refseq (GCF_000003025.5): ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/003/025/GCF_000003025.5_Sscrofa10.2/
UCSC Assembly susScr3
Local Assembly susScr3
Bowtie Idx s_scrofa_susScr3
liftOver susScr3ToHg19, susScr3ToHg38, susScr3ToMm10
RepeatMasker rmsk/rmsk_susScr3.SGA.gz
MGA FTP none
UCSC Genome Browser https://genome.ucsc.edu/cgi-bin/hgTracks?db=susScr3
Assembly support status partial

X. tropicalis (Nov 2009 v4.2/xenTro3)

NCBI Assembly https://www.ncbi.nlm.nih.gov/assembly/GCF_000004195.1/
NCBI Version v4.2
Source Assembled chromosomes from Refseq (GCF_000004195.1)
UCSC Assembly xenTro3
Local Assembly xenTro3
Bowtie Idx x_tropicalis_xenTro3
liftOver xenTro3ToHg19, xenTro3ToMm10, xenTro3ToMm9, xenTro3ToDanRer7
RepeatMasker rmsk/rmsk_xenTro3.SGA.gz
MGA FTP none
UCSC Genome Browser https://genome.ucsc.edu/cgi-bin/hgTracks?db=xenTro3
Assembly support status partial

X. tropicalis (Jul 2016 Xenopus_tropicalis_v9.1/xenTro9)

NCBI Assembly https://www.ncbi.nlm.nih.gov/assembly/GCF_000004195.3/
NCBI Version Xenopus_tropicalis_v9.1
Source Assembled chromosomes from Refseq (GCF_000004195.3): ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/004/195/GCF_000004195.3_Xenopus_tropicalis_v9.1/
UCSC Assembly none
Local Assembly xenTro9
Bowtie Idx x_tropicalis_xenTro9
liftOver none
RepeatMasker none
MGA FTP none
UCSC Genome Browser none
Assembly support status basic

Z. mays (Oct 2013 B73 RefGen_v3/zm3)

NCBI Assembly https://www.ncbi.nlm.nih.gov/assembly/GCF_000005005.1/
NCBI Version B73 RefGen_v3
Source Assembled chromosomes from RefSeq (GCF_000005005.1): ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/005/005/GCF_000005005.1_B73_RefGen_v3/
UCSC Assembly none (zeaMay_b73)
Local Assembly zm3
Bowtie Idx z_mays_zm3
liftOver none
RepeatMasker none
MGA FTP ftp://ccg.vital-it.ch/mga/zm3/
UCSC Genome Browser http://genome.ucsc.edu/cgi-bin/hgTracks?genome=zm3&hubUrl=http://epd.vital-it.ch/ucsc/epdHubCustomSpecies/epdHubCustomSpecies.txt
Assembly support status full

Last update: 9 Oct 2017