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Genome Indexes

This is a list of genomes that have been suggested for support in Galaxy.  
These are mostly large reference sequences that require lots of time and disk space to index for mapping tools.

The table shows whether the index has been generated for the galaxy tool:
    - dev - indicates the index has been generated
    - test - the index is available on the staging instance of galaxy and being tested 
    - PROD - the index is available on the production Galaxy and is available to all users
( Many genome applications build a special index into the reference genome in order to perform mapping.  Building such an index occurs once and may take hours for a large genome sequence, but allows sequences to be mapped quickly. )


If there is a large genome you need,  send an email to help@msi.umn.edu 
subject: Galaxy genome request <genome name>
Please include   
    genome name  
    assembly version
    URL for the genome source  (preferably a single fasta with a sequence for each chromosome)
( These requests require changes to the galaxy configuration and a restart of galaxy, so requests may take several weeks. )


For smaller genome sequences such as bacterial, archeal, small fungal, or viral genome sequences you can either upload the sequence yourself, or request MSI to add the reference to the "Shared Data" library, which you could then import to your history.  Most tools allow you to select references from your history as well as the "built in" or "locally cached".  Building a bowtie index for a bacteria-sized genome only requires seconds of time, so it can be done on the fly.  

You might want to do create a "Custom build" when using a genome reference from your history.  This allows to set the Database/Build attribute of datasets to your custom build name, and to use that name for visualizing results in the galaxy Track browser.  Under the "User" menu tab, select "Custom builds" and create a "Custom Database/Build" entry for this genome reference.  You will need a 2-column file that gives the name of each chromosome/contig in the reference assembly and the base pair length of that sequence.  You can use the "Compute sequence length" tool in the "FASTA manipulation" 
category to generate the Chromosome length file.
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Data sourceNameversionseqbwabowtiesamlastzgmap
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Data sourceNameversionseqbwabowtiesamlastzgmap
M Macaque        
G Gorilla        
N Bread mold        
MIPS Ustilago maydis Ustilago_maydis1 PROD PROD PROD PROD PROD PROD 
JGI Nectria haematococca Fusarium_solani_Necha2 PROD PROD PROD PROD PROD PROD 
NCBI Fusarium oxysporum f. sp. lycopersici 4287 Fusarium_oxysporum18813 PROD PROD PROD PROD PROD PROD 
NCBI Gibberella moniliformis 7600  Fusarium_verticillioides15553 PROD PROD PROD PROD PROD PROD 
NCBI Gibberella zeae Fusarium_graminearum243 PROD PROD PROD PROD PROD PROD 
JGI Populus trichocarpa  Ptrichocarpa_156 PROD PROD PROD PROD PROD PROD 
JGI Maize Zmays_121 PROD PROD PROD PROD PROD PROD 
UCSC Human hg19 PROD PROD PROD PROD PROD PROD 
UCSC Mouse mm9 PROD PROD PROD PROD PROD PROD 
UCSC Mouse mm8 PROD PROD PROD PROD PROD PROD 
UCSC Human hg18 PROD PROD PROD PROD PROD PROD 
UCSC Chimp panTro2 PROD PROD PROD PROD PROD PROD 
UCSC Cow bosTau4 PROD PROD PROD PROD PROD PROD 
UCSC Pig susScr2 PROD PROD PROD PROD PROD PROD 
UCSC Dog canFam2 PROD PROD PROD PROD PROD PROD 
UCSC Cat felCat3 PROD PROD PROD PROD PROD PROD 
UCSC Chicken galGal3 PROD PROD PROD PROD PROD PROD 
UCSC Horse equCab2 PROD PROD PROD PROD PROD PROD 
UCSC Opossum monDom5 PROD PROD PROD PROD PROD PROD 
UCSC Zebrafish danRer6 PROD PROD PROD PROD PROD PROD 
UCSC Fugu fr2 PROD PROD PROD PROD PROD PROD 
UCSC Frog xenTro2 PROD PROD PROD PROD PROD PROD 
UCSC HoneyBee apiMel3 PROD PROD PROD PROD PROD PROD 
UCSC Rat rn4 PROD PROD PROD PROD PROD PROD 
Ensembl Rice MSU6 PROD PROD PROD PROD PROD PROD 
Ensembl Rice  Jan_2005 PROD PROD PROD PROD PROD PROD 
UCSC Fruit fly dm3 PROD PROD PROD PROD PROD PROD 
UCSC Zebra_finch taeGut1 PROD PROD PROD PROD PROD PROD 
UCSC Yeast sacCer2 PROD PROD PROD PROD PROD PROD 
Ensembl Roundworm WS200 PROD PROD PROD PROD PROD PROD 
NCBIRest Ecoli eschColi_K12 PROD PROD PROD PROD PROD PROD 
JGI Soybean Gmax_109 PROD PROD PROD PROD PROD PROD 
BROAD Cryptococcus neoformans Cryptococcus_neoformans_grubii_H99 PROD PROD PROD PROD PROD PROD 
TGAC Pig Sscrofa10 PROD PROD PROD PROD PROD PROD 
CBCB Cow Bos_taurus_UMD_3.1 PROD PROD PROD PROD PROD PROD 
CGD Candida C_albicans_SC5314 PROD PROD PROD PROD PROD PROD 
JGI Medicago Mtruncatula_135 PROD PROD PROD PROD PROD PROD 
UCSC Rabbit oryCun2 PROD PROD PROD PROD PROD PROD 
Ensembl Turkey Meleagris gallopavo Turkey_2.01 PROD PROD PROD PROD PROD PROD 
MSU Potato Stuberosum_DM_v3 PROD PROD PROD PROD PROD PROD 
GDR Apple Malus_domestica1 PROD PROD PROD PROD PROD PROD 
MaizeSequence Maize ZmB73v2 dev dev dev dev dev dev 
Ensembl Thale cress Arabidopsis thaliana araTha_tair9 PROD PROD PROD PROD PROD PROD 
Ensembl Thale cress Arabidopsis thaliana Arabidopsis_thaliana_TAIR10       
NCBI Pig Sscrofa10.2 PROD PROD PROD PROD PROD PROD 
JGI Brachypodium distachyon brome grass brachy1.0 dev dev dev dev dev  
Showing 49 items
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