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

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 (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 full

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

G. gallus (Dec 2015 Gallus_gallus-5.0/galGal5)

NCBI Assembly https://www.ncbi.nlm.nih.gov/assembly/GCF_000002315.4/
NCBI Version Gallus_gallus-5.0
Source Assembled chromosomes from RefSeq (GCF_000002315.4): ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/315/GCF_000002315.4_Gallus_gallus-5.0/
UCSC Assembly galGal5
Local Assembly galGal5
Bowtie Idx g_gallus_galGal5
liftOver galGal5ToDanRer10, galGal5ToHg38, galGal5ToMm10, galGal5ToRn6, galGal5ToXenTro9
RepeatMasker rmsk/rmsk_galGal5.SGA.gz
MGA FTP ftp://ccg.vital-it.ch/mga/galGal5/
UCSC Genome Browser https://genome.ucsc.edu/cgi-bin/hgTracks?db=galGal5
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, hg19ToRheMac8
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, hg38ToGalGal5, hg38ToPanTro5, hg38ToRn5, hg38ToRn6, hg38ToSusScr3, hg38ToRheMac8
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, mm10ToGalGal5, mm10ToDanRer10, mm10ToDanRer7, mm10ToOreNil2, mm10ToPanTro5, mm10ToRn5, mm10ToRn6, mm10ToSusScr3, mm10ToRheMac8
RepeatMasker rmsk/rmsk_mm10.SGA.gz
MGA FTP ftp://ccg.vital-it.ch/mga/mm10/
UCSC Genome Browser https://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10
Assembly support status full

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

M. mulatta (Nov 2015 BCM Mmul_8.0.1/rheMac8)

NCBI Assembly https://www.ncbi.nlm.nih.gov/assembly/GCF_000772875.2/
NCBI Version Mmul_8.0.1
Source Assembled chromosomes from RefSeq (GCF_000772875.2): ftp://ftp.ncbi.nlm.nih.gov/genomes/Macaca_mulatta/Assembled_chromosomes
UCSC Assembly rheMac8
Local Assembly rheMac8
Bowtie Idx m_mulatta_rheMac8
liftOver rheMac8ToHg19, rheMac8ToHg38, rheMac8ToMm10, rheMac8ToPanTro5, rheMac8ToRn6
RepeatMasker rmsk/rmsk_rheMac8.SGA.gz
MGA FTP ftp://ccg.vital-it.ch/mga/rheMac8/
UCSC Genome Browser https://genome.ucsc.edu/cgi-bin/hgTracks?db=rheMac8
Assembly support status full

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, rn6ToMm10, rn6ToBosTau8, rn6ToCanFam3, rn6ToPanTro5, rn6ToDanRer10, rn6ToGalGal5, rn6ToRheMac8
RepeatMasker rmsk/rmsk_rn6.SGA.gz
MGA FTP ftp://ccg.vital-it.ch/mga/rn6/
UCSC Genome Browser https://genome.ucsc.edu/cgi-bin/hgTracks?db=rn6
Assembly support status full

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

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: 16 Jul 2018