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Revision 152 - (hide annotations)
Mon Mar 29 13:33:06 2021 UTC (2 weeks, 2 days ago) by nfreese
File size: 10068 byte(s)
IGBF-2803:Add Ficedula albicollis genome;Mar 29, 2021
1 aloraine 66 Options +Indexes
2     IndexOptions FancyIndexing HTMLTable SuppressRules
3     IndexOptions IconsAreLinks ScanHTMLTitles NameWidth=* DescriptionWidth=*
4    
5     # Autoindex-Strapdown Directives
6     AddType text/plain .md
7     HeaderName HEADER.md
8     ReadmeName README.md
9    
10     # Customize by setting theme and title
11     IndexHeadInsert "<script>conf = {theme: 'united', title: 'Integrated Genome Browser QuickLoad Site'};</script> \
12     strapdown: '/styling/strapdown/v/0.2/strapdown.js'};</script> \
13     <script src='/styling/autoindex_strapdown.js'></script> \
14     <link rel='stylesheet' href='/styling/autoindex_strapdown.css'>"
15    
16     # Icons using Bootstrap's Glyphicon set
17     DefaultIcon /styling/icons/glyphicon-file.svg
18     AddIcon /styling/icons/blank.svg ^^BLANKICON^^
19     AddIcon /styling/icons/glyphicon-folder-open.svg ^^DIRECTORY^^
20     AddIcon /styling/icons/glyphicon-circle-arrow-up.svg ..
21     AddIconByType (TXT,/styling/icons/glyphicon-file.svg) text/*
22     AddIconByType (IMG,/styling/icons/glyphicon-picture.svg) image/*
23     AddIconByType (SND,/styling/icons/glyphicon-music.svg) audio/*
24     AddIconByType (VID,/styling/icons/glyphicon-film.svg) video/*
25    
26     IndexIgnore HEADER* README* FOOTER* /styling *~ *#
27     AddDescription "Tells search engines what to ignore" robots.txt
28     AddDescription "Taxonomic and common names for species, shown in IGB species menu" species.txt
29     AddDescription "Chromosome synonyms" chromosome.txt
30     AddDescription "Lists size of largest transcript, for RNA-Seq normalization" tx_sizes.txt.gz
31     AddDescription "Icon IGB displays for this data source in the Data Access tab" favicon.ico
32     AddDescription "Sequence data in blat 2bit format" *.2bit
33     AddDescription "Sequence data in fastq format" *.fastq.gz
34     AddDescription "BedGraph (wiggle) format file" *.wig.gz
35     AddDescription "BedGraph (wiggle) format file" *.bedgraph.gz
36     AddDescription "Cytobands file" cytoBand.cyt
37     AddDescription "Tabix index file" *.gz.tbi
38     AddDescription "PSL (alignments) blat output file" *.psl.gz
39     AddDescription "Loraine Lab FindJunctions file" *.FJ.bed.gz
40     AddDescription "Data from UCSC refGene table" *_refGene.bed.gz
41     AddDescription "Annotation or junction file" *.bed.gz
42     AddDescription "Annotation or junction file" *.bed
43     AddDescription "EST alignments" EST
44     AddDescription "mRNA alignments" mRNA
45 aloraine 93 AddDescription "Anguilla rostrata" (Oct 2016) American eel (LTYT01/Dryad)" A_rostrata_Oct_2016
46     AddDescription "Anopheles gambiae (Oct 2006) mosquito (AgamP3/anoGam3)" A_gambiae_Oct_2006
47 aloraine 66 AddDescription "Anopheles gambiae (Feb 2003) mosquito (anoGam1/IAGP v.MOZ2)" A_gambiae_Feb_2003
48     AddDescription "Ailuropoda melanoleuca (Dec 2009) giant panda (ailMel1/BGI-Shenzhen AilMel 1.0)" A_melanoleuca_Dec_2009
49     AddDescription "Apis mellifera (honeybee) Jan 2005 (apiMel2/Baylor College of Medicine HGSC v.Amel_2.0 )" A_mellifera_Jan_2005
50     AddDescription "Arabidopsis thaliana TAIR9, TAIR10 genome assembly" A_thaliana_Jun_2009
51     AddDescription "Arabidopsis thaliana TAIR8 genome assembly" A_thaliana_Apr_2008
52     AddDescription "Arabidopsis thaliana TIGR5 genome assembly" A_thaliana_Jan_2004
53     AddDescription "Slime mold" D_discoideum
54     AddDescription "Medicago truncatula" M_truncatula_Mar_2009
55     AddDescription "Castor bean" R_communis
56     AddDescription "Arabidopsis lyrata JGI v1.0 assembly" A_lyrata_Apr_2011
57     AddDescription "Escherichia coli K12-MG1655" E_coli_K12-MG1655_Jan_2012
58     AddDescription "Fragaria vesca (woodland strawberry) v1.1" F_vesca_Sep_2011
59     AddDescription "Cavia porcellus (Feb 2008) guinea pig (cavPor3)" C_porcellus_Feb_2008
60 aloraine 88 AddDescription "C. elegans Feb 2013 (WBcel235/ce11)" C_elegans_Feb_2013
61 aloraine 66 AddDescription "C. elegans Oct 2010 (WS220/ce10)" C_elegans_Oct_2010
62 aloraine 93 AddDescription "Chlorocebus sabaeus (Mar 2014) African green monkey (Chlorocebus_sabaeus 1.1/chlSab2)" C_sabaeus_Mar_2014
63 aloraine 87 AddDescription "Danio rerio (May 2017) zebrafish (GRCz11/danRer11)" D_rerio_May_2017
64 aloraine 66 AddDescription "Danio rerio (Jul 2010) zebrafish (danRer7/Zv9)" D_rerio_Jul_2010
65 aloraine 104 AddDescription "Daphnia magna Xinb3 v2.4 (Apr 2010) water flea" D_magna_Apr_2010
66     AddDescription "Daphnia magna SK v1.0 (Jan 2019) water flea" D_magna_Jan_2019
67     AddDescription "Daphnia pulex TCO v1.0 (Feb 2011) water flea" D_pulex_Feb_2011
68     AddDescription "Daphnia pulex PA42 v3.0 (Sep 2016) water flea" D_pulex_Sep_2016
69 aloraine 66 AddDescription "Drosophila melanogaster (Apr 2006) fruit fly (dm3/BDGP R5)" D_melanogaster_Apr_2006
70     AddDescription "Drosophila melanogaster (July 2014) fruit fly (dmel_r6.03_FB2014_06)" D_melanogaster_Jul_2014
71     AddDescription "Equus caballus (Sep 2007) horse (equCab2)" E_caballus_Sep_2007
72     AddDescription "Felis catus (Dec 2008) cat (NHGRI/GTB V17e/felCat4)" F_catus_Dec_2008
73 nfreese 152 AddDescription "Ficedula albicollis (Jun 2013) collared flycatcher (FicAlb1.5)" F_albicollis_Jun_2013
74 aloraine 66 AddDescription "Gallus gallus (Nov 2011) chicken (galGal4/ICGC Gallus-gallus-4.0)" G_gallus_Nov_2011
75     AddDescription "Loxodonta africana (Jul 2009) elephant (loxAfr3)" L_africana_Jul_2009
76     AddDescription "Papaya" C_papaya_Aug_2010
77     AddDescription "Brachypodium distachyon (a model grass) JGI v1.0 8x assembly" B_distachyon_Aug_2010
78     AddDescription "Homo sapiens hg38 (Genome Reference Consortium GRCh38)" H_sapiens_Dec_2013
79     AddDescription "Homo sapiens hg19 (Genome Reference Consortium GRCh37)" H_sapiens_Feb_2009
80     AddDescription "Homo sapiens hg18 (Genome Reference Consortium GRCh36)" H_sapiens_Mar_2006
81     AddDescription "Homo sapiens hg17 (Genome Reference Consortium GRCh35)" H_sapiens_May_2004
82     AddDescription "Nematostella vectensis, starlet sea anemone" N_vectensis_Jun_2007
83     AddDescription "Chlamy (an algal genome)" C_reinhardtii_Nov_2010
84     AddDescription "Camelina, false flax, an oilseed crop" C_sativa_DH55_Apr_2014
85 aloraine 122 AddDescription "Cannabis sativa CBDRx Dec 2018" C_sativa_CBDRx_Dec_2018
86 aloraine 66 AddDescription "Rice, japonic variety" O_sativa_japonica_Jun_2009
87     AddDescription "Rice, japonic variety Os-Nipponbare-Reference-IRGSP-1.0 assembly" O_sativa_japonica_Oct_2011
88     AddDescription "Soybean Glyma1" G_max_Aug_2010
89     AddDescription "Soybean Glyma2" G_max_Jan_2014
90 aloraine 84 AddDescription "S. cerevisiae strain S288C (Apr 2011) budding yeast (sacCer3)" S_cerevisiae_Apr_2011
91     AddDescription "S. cerevisiae strain S288C (Jun 2008) budding yeast (sacCer2)" S_cerevisiae_Jun_2008
92 aloraine 66 AddDescription "Fission yeast" S_pombe_Aug_2007
93     AddDescription "Volvox" V_carteri_Jul_2010
94     AddDescription "Wine grape 12x assembly" V_vinifera_Mar_2010
95     AddDescription "Physcomitrella patens (moss)" P_patens_Jan_2008
96 aloraine 141 AddDescription "Physcomitrella patens (moss) v3.3" P_patens_Jan_2018
97 aloraine 66 AddDescription "Black cottonwood (poplar)" P_trichocarpa_Aug_2012
98     AddDescription "Black cottonwood (poplar)" P_trichocarpa_Jan_2010
99     AddDescription "Sorghum bicolor" S_bicolor_Jan_2009
100     AddDescription "Sorghum bicolor" S_bicolor_Jun_2013
101 aloraine 93 AddDescription "Candida albicans WO-1 (Dec 2013)" C_albicans_WO-1_Dec_2013
102 aloraine 66 AddDescription "Candida albicans" C_albicans
103     AddDescription "Zea mays B73 RefGen_v2 assembly" Z_mays_B73_Mar_2010
104 aloraine 85 AddDescription "Bos taurus (Jun 2014) cow (UMD_3.1.1/bosTau8)" B_taurus_Jun_2014
105 aloraine 66 AddDescription "Bos taurus (cow) bosTau7 Oct 2011 assembly" B_taurus_Oct_2011
106     AddDescription "C. elegans May 2008 WS190/ce6" C_elegans_May_2008
107     AddDescription "Annotation and data file list" annots.[txt|xml]
108     AddDescription "Chromosome lengths and assembly information" mod_chromInfo.txt
109     AddDescription "Chromosome lengths and assembly information" genome.txt
110     AddDescription "IGB synonym file" synonyms.txt
111     AddDescription "Available genome assemblies and their titles" contents.txt
112     AddDescription "Mitochondrial Genome (Fasta format)" [Cc]hrM.fa*
113     AddDescription "Chloroplast Genome (Fasta format)" [Cc]hrC.fa*
114     AddDescription "Peach v1 genome assembly" P_persica_Apr_2010
115     AddDescription "Thermococcus kodakaraensis" T_kodakaraensis_KOD1_May_2004
116     AddDescription "Xenopus tropicalis JGI 4.2/xenTro3" X_tropicalis_Nov_2009
117 aloraine 115 AddDescription "Xenopus tropicalis JGI 9.1/xenTro9" X_tropicalis_Jul_2016
118 aloraine 66 AddDescription "Mus musculus (Dec 2011) mouse (GRCm38/mm10)" M_musculus_Dec_2011
119     AddDescription "Mus musculus (Jul 2007) mouse (NCBI37/mm9)" M_musculus_Jul_2007
120     AddDescription "Mus musculus (Feb 2006) mouse (NCBI36/mm8)" M_musculus_Feb_2006
121 aloraine 77 AddDescription "Mus musculus (Aug 2005) mouse (NCBI35/mm7)" M_musculus_Aug_2005
122 aloraine 66 AddDescription "Malus domestica (Jun 2017) apple" M_domestica_Borkh_Jun_2017
123     AddDescription "Musa acuminata DH Pahang (Jan 2016) banana (v2)" M_acuminata_DH_Pahang_Jan_2016
124     AddDescription "Pan troglodytes (Oct 2010) chimpanzee (CGSC 2.1.3/panTro3)" P_troglodytes_Oct_2010
125     AddDescription "Ovis aries (Feb 2010) sheep (ISGC Ovis_aries_1/oviAri1)" O_aries_Feb_2010
126 aloraine 83 AddDescription "Rattus norvegicus (Jul 2014) rat (RGSC 6.0/rn6)" R_norvegicus_Jul_2014
127 aloraine 119 AddDescription "Rattus norvegicus (Mar 2012) rat (RGSC 5.0/rn5)" R_norvegicus_Mar_2012
128     AddDescription "Solanum lycopersicum (Sep 2019) tomato (SL4.0)" S_lycopersicum_Sep_2019
129 aloraine 66 AddDescription "Solanum lycopersicum (Feb 2017) tomato (SL3.0)" S_lycopersicum_Feb_2017
130     AddDescription "Solanum lycopersicum (Feb 2014) tomato (SL2.50)" S_lycopersicum_Feb_2014
131     AddDescription "Solanum lycopersicum (May 2012) tomato (SL2.40)" S_lycopersicum_May_2012
132     AddDescription "S. pombe (May 2012) fission yeast" S_pombe_May_2012
133     AddDescription "Takifugu rubripes (Oct 2011) Fugu (FUGU5/fr3)" T_rubripes_Oct_2011
134     AddDescription "Thellungiella parvula (salt cress) v2, May 2012" T_parvula_May_2012
135     AddDescription "Felis catus (Sep 2011) cat (ICGSC Felis_catus 6.2/felCat5)" F_catus_Sep_2011
136 aloraine 84 AddDescription "Solanum tuberosum Group Phureja clone DM1-3 (potato) v4.03" S_tuberosum_DM_Jul_2011
137 aloraine 66 AddDescription "Tribolium castaneum (March 2008) red flour beetle" T_castaneum_Mar_2008
138     AddDescription "Lotmaria passim, strain SF, Crithidia mellificae strain SF, whole genome shotgun sequencing project" L_passim_Apr_2014
139     AddDescription "Yarrowia lipolytica CLIB122 (Jul 2004) Assembly GCA_000002525.2" Y_lipolytica_CLIB122_Jul_2004
140     AddDescription "Yarrowia lipolytica PO1f (May 2014) Assembly GCA_000590845.2" Y_lipolytica_PO1f_May_2014
141     AddDescription "Yarrowia lipolytica WSH-Z06 (Mar 2014) Assembly GCA_000613155.1" Y_lipolytica_WSH-Z06_Mar_2014
142 aloraine 124 AddDescription "Triticum aestivum (IWGSC v1)" T_aestivum_Aug_2018

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