strapdown: '/styling/strapdown/v/0.2/strapdown.js'}; 
<html>
<title>Integrated Genome Browser QuickLoad Site</title>
<body>
<h1>Welcome to IGB Quickload Main</h1>
<p>
Data available here are configured for visualization
in the <a href="https://bioviz.org">Integrated Genome Browser</a>.
These data include gene annotation files and genome information for 
many plant, animal, and microbial species.</p>
<p>When IGB launches, it contacts a deployed copy of Quickload Main and retrieves
a file "<a href="./contents.txt">contents.txt</a>" that lists all genome assemblies available for
display in IGB.
</p>
<p>
The data here are version-controlled using subversion, a centralized version-control system that
attaches versions to individual files and supports checking out parts of the repository. To browse
the subversion repository hosting these data, visit 
<a href="https://svn.bioviz.org/viewvc/genomes/quickload">https://svn.bioviz.org/viewvc/genomes/quickload/</a>.</p>
<h2>About Quickload</h2>
<p>
A Quickload site is a simple system of directories, sequence files, and
annotation files formatted for visualization in Integrated Genome Browser. It's a convenient
way to share data sets with other labs and with the public. IGB can display the contents of
many Quickload sites at the same time. This makes it easy to compare data across experiments.
This makes IGB an "integrated" genome browser. 
</p>
<h2>About this site</h2>
<p>
This site is a checked-out copy of Quickload Main subversion repository, deployed in the "htdocs" directory
of the apache2 Web server. 
 </p>
<p>
To make the Quickload data contents easy to browse, the repository also includes styling configurations using
javascript and CSS. 
</p>

<h2>How to get a copy</h2> 
<p>Install svn and check out the repository with a read-only user:</p>
<p>`svn co --username=guest https://svn.bioviz.org/repos/genomes/quickload`</p>
<p>When prompted, enter username "guest" and password "guest".</p> 

<h2>Test a checked-out copy in Integrated Genome Browser</h2>
<p>Open Integrated Genome Browser and select <B>Preferences</B> from the <B>File</B> menu. Select the <B>Data Sources</B> tab. Add the checked-out root directory as a new Quickload Data Source. The folder containing the file "contents.txt" is the Quickload root directory.</p>
<h2>Add too big 2bit files</h2>
<p>Some genome sequence files are so large that they are not version-controlled. One such file
is `T_aestivum_Aug_2018.2bit`, a wheat genome assembly sequence file. To enable IGB users to view
sequence data from this genome, add the file to directory `quickload/T_aestivum_Aug_2018`.</p> 
<hr/>
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[ICO]NameLast modifiedSizeDescription
[PARENTDIR]Parent Directory  -  
[DIR]A_melanoleuca_Dec_2009/2023-06-16 13:30 - Ailuropoda melanoleuca (Dec 2009) giant panda (ailMel1/BGI-Shenzhen AilMel 1.0)
[DIR]A_rostrata_Oct_2016/2023-06-16 13:31 - Anguilla rostrata
[DIR]A_gambiae_Feb_2003/2023-06-16 14:06 - Anopheles gambiae (Feb 2003) mosquito (anoGam1/IAGP v.MOZ2)
[DIR]A_gambiae_Oct_2006/2023-06-16 13:18 - Anopheles gambiae (Oct 2006) mosquito (AgamP3/anoGam3)
[DIR]A_mellifera_Jan_2005/2023-06-16 13:18 - Apis mellifera (honeybee) Jan 2005 (apiMel2/Baylor College of Medicine HGSC v.Amel_2.0 )
[DIR]A_lyrata_Apr_2011/2023-06-16 14:26 - Arabidopsis lyrata JGI v1.0 assembly
[DIR]A_thaliana_Apr_2008/2023-06-16 14:17 - Arabidopsis thaliana TAIR8 genome assembly
[DIR]A_thaliana_Jun_2009/2023-06-16 13:23 - Arabidopsis thaliana TAIR9, TAIR10 genome assembly
[TXT]contents.txt2024-07-13 17:58 6.3KAvailable genome assemblies and their titles
[DIR]P_trichocarpa_Aug_2012/2023-06-16 14:09 - Black cottonwood (poplar)
[DIR]P_trichocarpa_Jan_2010/2023-06-16 13:23 - Black cottonwood (poplar)
[DIR]B_taurus_Jun_2014/2023-06-16 13:22 - Bos taurus (Jun 2014) cow (UMD_3.1.1/bosTau8)
[DIR]B_taurus_Oct_2011/2023-06-16 13:40 - Bos taurus (cow) bosTau7 Oct 2011 assembly
[DIR]B_distachyon_Aug_2010/2023-06-16 14:27 - Brachypodium distachyon (a model grass) JGI v1.0 8x assembly
[DIR]C_elegans_Feb_2013/2023-06-16 14:06 - C. elegans Feb 2013 (WBcel235/ce11)
[DIR]C_elegans_May_2008/2023-06-16 14:05 - C. elegans May 2008 WS190/ce6
[DIR]C_elegans_Oct_2010/2023-06-16 13:18 - C. elegans Oct 2010 (WS220/ce10)
[DIR]C_sativa_DH55_Apr_2014/2023-06-16 13:35 - Camelina, false flax, an oilseed crop
[DIR]C_albicans_SC5314_Jun_2014/2023-06-16 13:45 - Candida albicans
[DIR]C_albicans_SC5314_Nov_2008/2023-06-16 13:30 - Candida albicans
[DIR]C_albicans_WO-1_Jul_2010/2023-06-16 14:01 - Candida albicans
[DIR]C_albicans_WO-1_Dec_2013/2023-06-16 14:06 - Candida albicans WO-1 (Dec 2013)
[DIR]C_sativa_CBDRx_Dec_2018/2023-06-16 14:26 - Cannabis sativa CBDRx Dec 2018
[DIR]R_communis_May_2008/2023-06-16 13:36 - Castor bean
[DIR]C_porcellus_Feb_2008/2023-06-16 14:24 - Cavia porcellus (Feb 2008) guinea pig (cavPor3)
[DIR]C_reinhardtii_Nov_2010/2023-06-16 14:13 - Chlamy (an algal genome)
[DIR]C_sabaeus_Mar_2014/2023-06-16 14:17 - Chlorocebus sabaeus (Mar 2014) African green monkey (Chlorocebus_sabaeus 1.1/chlSab2)
[DIR]D_rerio_Jul_2010/2023-06-16 14:25 - Danio rerio (Jul 2010) zebrafish (danRer7/Zv9)
[DIR]D_rerio_May_2017/2023-06-16 13:45 - Danio rerio (May 2017) zebrafish (GRCz11/danRer11)
[DIR]D_magna_Jan_2019/2023-06-16 14:01 - Daphnia magna SK v1.0 (Jan 2019) water flea
[DIR]D_magna_Apr_2010/2023-06-16 13:36 - Daphnia magna Xinb3 v2.4 (Apr 2010) water flea
[DIR]D_pulex_Sep_2016/2023-06-16 14:32 - Daphnia pulex PA42 v3.0 (Sep 2016) water flea
[DIR]D_pulex_Feb_2011/2023-06-16 13:52 - Daphnia pulex TCO v1.0 (Feb 2011) water flea
[DIR]D_melanogaster_Apr_2006/2023-06-16 13:41 - Drosophila melanogaster (Apr 2006) fruit fly (dm3/BDGP R5)
[DIR]D_melanogaster_Aug_2014/2024-06-04 09:51 - Drosophila melanogaster (Aug 2014) fruit fly (BDGP Release 6 + ISO1 MT/dm6)
[DIR]D_melanogaster_Jul_2014/2023-06-16 13:49 - Drosophila melanogaster (July 2014) fruit fly (dmel_r6.03_FB2014_06)
[DIR]E_caballus_Sep_2007/2023-06-16 13:24 - Equus caballus (Sep 2007) horse (equCab2)
[DIR]E_coli_K12-MG1655_Jan_2012/2023-06-16 13:53 - Escherichia coli K12-MG1655
[DIR]F_catus_Sep_2011/2023-06-16 14:19 - Felis catus (Sep 2011) cat (ICGSC Felis_catus 6.2/felCat5)
[DIR]F_albicollis_Jun_2013/2023-06-16 14:27 - Ficedula albicollis (Jun 2013) collared flycatcher (FicAlb1.5)
[DIR]F_vesca_Sep_2011/2023-06-16 13:34 - Fragaria vesca (woodland strawberry) v1.1
[DIR]G_gallus_Nov_2011/2023-06-16 13:15 - Gallus gallus (Nov 2011) chicken (galGal4/ICGC Gallus-gallus-4.0)
[DIR]H_sapiens_May_2004/2023-06-16 14:12 - Homo sapiens hg17 (Genome Reference Consortium GRCh35)
[DIR]H_sapiens_Mar_2006/2023-06-16 14:35 - Homo sapiens hg18 (Genome Reference Consortium GRCh36)
[DIR]H_sapiens_Feb_2009/2023-06-16 14:05 - Homo sapiens hg19 (Genome Reference Consortium GRCh37)
[DIR]H_sapiens_Dec_2013/2023-06-16 14:01 - Homo sapiens hg38 (Genome Reference Consortium GRCh38)
[DIR]H_exemplaris_Z151_Apr_2017/2024-05-01 15:23 - Hypsibius exemplaris strain Z151 (Apr 2017) water bear (nHd_3.1 assembly)
[TXT]synonyms.txt2024-07-13 17:58 458 IGB synonym file
[IMG]favicon.ico2023-06-16 14:21 7.1KIcon IGB displays for this data source in the Data Access tab
[DIR]L_passim_Apr_2014/2023-06-16 14:35 - Lotmaria passim, strain SF, Crithidia mellificae strain SF, whole genome shotgun sequencing project
[DIR]L_africana_Jul_2009/2023-06-16 13:48 - Loxodonta africana (Jul 2009) elephant (loxAfr3)
[DIR]M_domestica_Borkh_Jun_2017/2023-06-16 13:42 - Malus domestica (Jun 2017) apple
[DIR]M_truncatula_Mar_2009/2023-06-16 13:23 - Medicago truncatula
[DIR]M_musculus_Aug_2005/2023-06-16 14:21 - Mus musculus (Aug 2005) mouse (NCBI35/mm7)
[DIR]M_musculus_Dec_2011/2023-06-16 13:27 - Mus musculus (Dec 2011) mouse (GRCm38/mm10)
[DIR]M_musculus_Feb_2006/2023-06-16 13:34 - Mus musculus (Feb 2006) mouse (NCBI36/mm8)
[DIR]M_musculus_Jul_2007/2023-06-16 14:32 - Mus musculus (Jul 2007) mouse (NCBI37/mm9)
[DIR]M_musculus_Jun_2020/2023-07-24 18:36 - Mus musculus (Jun 2020) mouse (GRCm39/mm39)
[DIR]M_acuminata_DH_Pahang_Jan_2016/2023-06-16 13:49 - Musa acuminata DH Pahang (Jan 2016) banana (v2)
[DIR]N_vectensis_Jun_2007/2023-06-16 13:48 - Nematostella vectensis, starlet sea anemone
[DIR]O_aries_Feb_2010/2023-06-16 13:43 - Ovis aries (Feb 2010) sheep (ISGC Ovis_aries_1/oviAri1)
[DIR]P_troglodytes_Oct_2010/2023-06-16 13:21 - Pan troglodytes (Oct 2010) chimpanzee (CGSC 2.1.3/panTro3)
[DIR]C_papaya_Aug_2010/2023-06-16 14:28 - Papaya
[DIR]P_persica_Apr_2010/2023-06-16 14:28 - Peach v1 genome assembly
[DIR]P_patens_Jan_2008/2023-06-16 13:49 - Physcomitrella patens (moss)
[DIR]P_patens_Jan_2018/2023-06-16 14:09 - Physcomitrella patens (moss) v3.3
[DIR]R_varieornatus_YOKOZUNA-1_Nov_2016/2024-07-13 17:58 - Ramazzottius varieornatus strain YOKOZUNA-1 (Nov 2016) water bear (Rvar_4.0 assembly)
[DIR]R_norvegicus_Jul_2014/2023-06-16 13:18 - Rattus norvegicus (Jul 2014) rat (RGSC 6.0/rn6)
[DIR]R_norvegicus_Mar_2012/2023-06-16 14:09 - Rattus norvegicus (Mar 2012) rat (RGSC 5.0/rn5)
[DIR]R_norvegicus_Nov_2020/2023-07-24 18:36 - Rattus norvegicus (Nov 2020) rat (mRatBN7.2/rn7)
[DIR]O_sativa_japonica_Jun_2009/2023-06-16 13:44 - Rice, japonic variety
[DIR]O_sativa_japonica_Oct_2011/2023-06-16 14:10 - Rice, japonic variety Os-Nipponbare-Reference-IRGSP-1.0 assembly
[DIR]S_cerevisiae_Apr_2011/2023-06-16 13:21 - S. cerevisiae strain S288C (Apr 2011) budding yeast (sacCer3)
[DIR]S_cerevisiae_Jun_2008/2023-06-16 13:34 - S. cerevisiae strain S288C (Jun 2008) budding yeast (sacCer2)
[DIR]S_pombe_May_2012/2024-04-09 15:35 - S. pombe (May 2012) fission yeast
[DIR]D_discoideum_Ax4_May_2009/2023-06-16 13:15 - Slime mold
[DIR]S_lycopersicum_Feb_2014/2023-06-16 13:14 - Solanum lycopersicum (Feb 2014) tomato (SL2.50)
[DIR]S_lycopersicum_Feb_2017/2023-06-16 13:16 - Solanum lycopersicum (Feb 2017) tomato (SL3.0)
[DIR]S_lycopersicum_Jun_2022/2024-06-04 09:51 - Solanum lycopersicum (Jun 2022) tomato (SL5.0)
[DIR]S_lycopersicum_May_2012/2023-06-16 13:25 - Solanum lycopersicum (May 2012) tomato (SL2.40)
[DIR]S_lycopersicum_Sep_2019/2024-06-04 09:51 - Solanum lycopersicum (Sep 2019) tomato (SL4.0)
[DIR]S_tuberosum_DM_Jul_2011/2023-06-16 13:19 - Solanum tuberosum Group Phureja clone DM1-3 (potato) v4.03
[DIR]S_bicolor_Jan_2009/2023-06-16 14:29 - Sorghum bicolor
[DIR]S_bicolor_Jun_2013/2023-06-16 13:37 - Sorghum bicolor
[DIR]G_max_Aug_2010/2023-06-16 14:13 - Soybean Glyma1
[DIR]G_max_Jan_2014/2023-06-16 13:36 - Soybean Glyma2
[DIR]T_rubripes_Oct_2011/2023-06-16 13:53 - Takifugu rubripes (Oct 2011) Fugu (FUGU5/fr3)
[TXT]species.txt2024-07-13 17:58 442 Taxonomic and common names for species, shown in IGB species menu
[DIR]T_parvula_May_2012/2023-06-16 14:28 - Thellungiella parvula (salt cress) v2, May 2012
[DIR]T_kodakaraensis_KOD1_May_2004/2023-06-16 13:36 - Thermococcus kodakaraensis
[DIR]T_castaneum_Mar_2008/2023-06-16 13:30 - Tribolium castaneum (March 2008) red flour beetle
[DIR]T_aestivum_Aug_2018/2023-07-28 09:57 - Triticum aestivum (IWGSC v1)
[DIR]V_carteri_Jul_2010/2023-06-16 13:18 - Volvox
[DIR]V_vinifera_Mar_2010/2023-06-16 14:14 - Wine grape 12x assembly
[DIR]X_tropicalis_Nov_2009/2023-06-16 13:41 - Xenopus tropicalis JGI 4.2/xenTro3
[DIR]X_tropicalis_Jul_2016/2023-06-16 13:15 - Xenopus tropicalis JGI 9.1/xenTro9
[DIR]Y_lipolytica_CLIB122_Jul_2004/2023-06-16 14:21 - Yarrowia lipolytica CLIB122 (Jul 2004) Assembly GCA_000002525.2
[DIR]Y_lipolytica_PO1f_May_2014/2023-06-16 14:06 - Yarrowia lipolytica PO1f (May 2014) Assembly GCA_000590845.2
[DIR]Y_lipolytica_WSH-Z06_Mar_2014/2023-06-16 13:19 - Yarrowia lipolytica WSH-Z06 (Mar 2014) Assembly GCA_000613155.1
[DIR]Z_mays_B73_Mar_2010/2023-06-16 13:51 - Zea mays B73 RefGen_v2 assembly
Apache/2.4.52 (Ubuntu) Server at igbquickload.org Port 80