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Update chrom.sizes files, for igvtools
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@jrobinso
jrobinso committed Aug 4, 2021
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Showing 32 changed files with 83,140 additions and 39 deletions.
11 changes: 5 additions & 6 deletions genomes/genomes.tab
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Expand Up @@ -27,7 +27,7 @@ D. melanogaster (dm3) https://s3.amazonaws.com/igv.org.genomes/dm3/dm3.json dm3
D. melanogaster (r5.9) https://s3.amazonaws.com/igv.org.genomes/dmel_r5.9/dmel_r5.9.json dmel_r5.9
Dog (canFam3) https://s3.amazonaws.com/igv.org.genomes/json/canFam3.json canFam3
E. coli K-12 MG1655 (NC_000913.2) https://s3.amazonaws.com/igv.broadinstitute.org/genomes/NC_000913.2.genome NC_000913.2
E. coli K-12 (NC_000913.3) https://s3.amazonaws.com/igv.broadinstitute.org/genomes/NC_000913.3.gbk NC_000913.3
E. coli K-12 (NC_000913.3) https://s3.amazonaws.com/igv.broadinstitute.org/genomes/NC_000913.3.gbk NC_000913
Ferret (MusPutFur1.0) https://s3.amazonaws.com/igv.broadinstitute.org/genomes/MusPutFur1.0.genome MusPutFur1.0
Francisella tularensis (NC_008601) https://s3.amazonaws.com/igv.broadinstitute.org/genomes/NC_008601.gbk NC_008601
Glycine max (v8.0) https://s3.amazonaws.com/igv.broadinstitute.org/genomes/gmax8.genome gmax8
Expand All @@ -39,7 +39,7 @@ Human (1kg, b37+decoy) https://s3.amazonaws.com/igv.broadinstitute.org/genomes/1
Human (b37) https://s3.amazonaws.com/igv.org.genomes/b37/b37.genome b37
Human Adenovirus C https://s3.amazonaws.com/igv.broadinstitute.org/genomes/NC_001405.genome NC_001405
Human Herpesvirus 4, Type 1 https://s3.amazonaws.com/igv.broadinstitute.org/genomes/HHV4_Type1.genome HHV4_Type1
Human Herpesvirus 4, Type 2 https://s3.amazonaws.com/igv.broadinstitute.org/genomes/HHV4_Type2.genome HHV4_Type2
Human Herpesvirus 4, Type 2 https://s3.amazonaws.com/igv.broadinstitute.org/genomes/HHV4_Type2.genome EBV_Type2
Human hg18 https://s3.amazonaws.com/igv.org.genomes/json/hg18.json hg18
Human hg19 https://s3.amazonaws.com/igv.org.genomes/json/hg19.json hg19
Human hg38 https://s3.amazonaws.com/igv.org.genomes/json/hg38.json hg38
Expand All @@ -59,7 +59,7 @@ N. Meningitidis (FAM18) https://s3.amazonaws.com/igv.broadinstitute.org/test/gen
N. Meningitidis (MC58) https://s3.amazonaws.com/igv.broadinstitute.org/test/genomes/NC_003112.genome NC_003112
N. Meningitidis (Z2491) https://s3.amazonaws.com/igv.broadinstitute.org/test/genomes/NC_003116.genome NC_003116
P. falciparum 3D7 (V9.0) https://s3.amazonaws.com/igv.broadinstitute.org/genomes/Pf3D7_v9.0.genome Pf3D7_v9.0
Plasmodium (3D7 V24) https://s3.amazonaws.com/igv.broadinstitute.org/genomes/PlasmoDB_24.genome Plasmodium_24
Plasmodium (3D7 V24) https://s3.amazonaws.com/igv.broadinstitute.org/genomes/PlasmoDB_24.genome PlasmoDB_24
Rabbit (oryCun2.0) https://s3.amazonaws.com/igv.broadinstitute.org/genomes/oryCun2.0.genome oryCun2.0
Rat (rn5) https://s3.amazonaws.com/igv.broadinstitute.org/genomes/rn5.genome rn5
Rat (rn6) https://s3.amazonaws.com/igv.org.genomes/json/rn6.json rn6
Expand All @@ -81,7 +81,7 @@ T. brucei gambiense https://s3.amazonaws.com/igv.broadinstitute.org/genomes/tbga
Tomato (2.31) https://s3.amazonaws.com/igv.broadinstitute.org/genomes/SL2.31.genome SL2.31
Tomato (2.40) https://s3.amazonaws.com/igv.broadinstitute.org/genomes/SL2.40.genome SL2.40
Trout (CCAF000000000) https://s3.amazonaws.com/igv.broadinstitute.org/genomes/CCAF000000000.genome CCAF000000000
V. vitifera https://s3.amazonaws.com/igv.broadinstitute.org/genomes/vvinifera.genome vvitifera
V. vitifera https://s3.amazonaws.com/igv.broadinstitute.org/genomes/vvinifera.genome vvinifera
X. tropicalis v9.0 https://s3.amazonaws.com/igv.broadinstitute.org/genomes/xenTro9.genome xenTro9
X. laevis (7.1) https://s3.amazonaws.com/igv.broadinstitute.org/genomes/laevis_7.1.genome laevis_7.1
Zebrafish (GRCz10/danRer10) https://s3.amazonaws.com/igv.org.genomes/json/danRer10.json danRer10
Expand All @@ -90,8 +90,6 @@ Zea mays (AGPv3.31) https://s3.amazonaws.com/igv.broadinstitute.org/genomes/AGPv
C. reinhardtii (CC-503 v5.5) https://s3.amazonaws.com/igv.org.genomes/Creinhardtii_CC-503_v5.0/2019-03-21_Creinhardtii_CC-503_v5.5.genome 2019-03-21_Creinhardtii_CC-503_v5.5
C. reinhardtii (CC-503 v5.6) https://s3.amazonaws.com/igv.org.genomes/C.reinhardtii_CC-503_v5.6+/2019-03-21_Creinhardtii_CC-503_v5.6.genome 2019-03-21_Creinhardtii_CC-503_v5.6
C. reinhardtii (CC-503 v5.6 Cp+Mt v4.4) https://s3.amazonaws.com/igv.org.genomes/Creinhardtii_CC-503_v5.6/2019-03-21_Creinhardtii_CC-503_v5.6_Cp%2BMt_v4.4.genome 2019-03-21_Creinhardtii_CC-503_v5.6_Cp+Mt_v4.4
Ixodes scapularis JCVI_ISG_i3_1.0 (GCA_000208615.1) https://s3.amazonaws.com/igv.org.genomes/tick/GCA_000208615.1/GCA_000208615.1.genome GCA_000208615.1
Ixodes scapularis ISE6_asm2.2_deduplicated (GCA_002892825.2) https://s3.amazonaws.com/igv.org.genomes/tick/GCA_000208615.1/GCA_000208615.1.genome GCA_002892825.2
SARS-CoV-2 https://s3.amazonaws.com/igv.org.genomes/json/ASM985889v3.json ASM985889v3
S. pombe (ASM294v2) https://s3.amazonaws.com/igv.org.genomes/json/ASM294v2.json ASM294v2
Gorilla (gorGor4) https://s3.amazonaws.com/igv.org.genomes/json/gorGor4.json gorGor4
Expand All @@ -100,3 +98,4 @@ Pig (SGSC Sscrofa11.1/susScr11) https://s3.amazonaws.com/igv.org.genomes/json/su
Dog (canFam5) https://s3.amazonaws.com/igv.org.genomes/canFam5/canFam5.json canFam5
Rat (rn7) https://s3.amazonaws.com/igv.org.genomes/rn7/rn7.json rn7
Gorilla (Kamilah_GGO_v0/gorGor6) https://s3.amazonaws.com/igv.org.genomes/gorGor6/gorGor6.json gorGor6
Ixodes scapularus (GCF_016920785.1) https://s3.amazonaws.com/igv.org.genomes/GCF_016920785.1/GCF_016920785.1.json GCF_016920785.1
5 changes: 1 addition & 4 deletions genomes/genomes.txt
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Expand Up @@ -48,7 +48,7 @@ Human Mito (NC_012920) https://s3.amazonaws.com/igv.broadinstitute.org/genomes/N
Human respiratory synctial virus https://s3.amazonaws.com/igv.broadinstitute.org/genomes/M74568.genome M74568
Macaca fascicularis (CE_1.0) https://s3.amazonaws.com/igv.broadinstitute.org/genomes/CE_1.0.genome CE_1.0
Macaca fascicularis (5.0) https://s3.amazonaws.com/igv.org.genomes/Macaca_fascicularis_5.0/Macaca_fascicularis_5.0.genome GCF_000364345.1
Mouse (129S1/SvImJ) https://s3.amazonaws.com/igv.broadinstitute.org/genomes/SvImJ.genome 129S1/SvImJ
Mouse (129S1/SvImJ) https://s3.amazonaws.com/igv.broadinstitute.org/genomes/SvImJ.genome SvImJ
Mouse mm39 https://s3.amazonaws.com/igv.org.genomes/mm39/mm39.genome mm39
Mouse mm10 https://s3.amazonaws.com/igv.org.genomes/mm10/mm10.genome mm10
Mouse mm8 https://s3.amazonaws.com/igv.broadinstitute.org/genomes/mm8.genome mm8
Expand Down Expand Up @@ -89,10 +89,7 @@ Zea mays (AGPv3.31) https://s3.amazonaws.com/igv.broadinstitute.org/genomes/AGPv
C. reinhardtii (CC-503 v5.5) https://s3.amazonaws.com/igv.org.genomes/Creinhardtii_CC-503_v5.0/2019-03-21_Creinhardtii_CC-503_v5.5.genome 2019-03-21_Creinhardtii_CC-503_v5.5
C. reinhardtii (CC-503 v5.6) https://s3.amazonaws.com/igv.org.genomes/C.reinhardtii_CC-503_v5.6+/2019-03-21_Creinhardtii_CC-503_v5.6.genome 2019-03-21_Creinhardtii_CC-503_v5.6
C. reinhardtii (CC-503 v5.6 Cp+Mt v4.4) https://s3.amazonaws.com/igv.org.genomes/Creinhardtii_CC-503_v5.6/2019-03-21_Creinhardtii_CC-503_v5.6_Cp%2BMt_v4.4.genome 2019-03-21_Creinhardtii_CC-503_v5.6_Cp+Mt_v4.4
Ixodes scapularis JCVI_ISG_i3_1.0 (GCA_000208615.1) https://s3.amazonaws.com/igv.org.genomes/tick/GCA_000208615.1/GCA_000208615.1.genome GCA_000208615.1
Ixodes scapularis ISE6_asm2.2_deduplicated (GCA_002892825.2) https://s3.amazonaws.com/igv.org.genomes/tick/GCA_000208615.1/GCA_000208615.1.genome GCA_002892825.2
SARS-CoV-2 https://s3.amazonaws.com/igv.org.genomes/SARS-CoV-2/ASM985889v3.genome ASM985889v3
Dog (canFam5) https://s3.amazonaws.com/igv.org.genomes/canFam5/canFam5.genome canFam5
Rat (rn7) https://s3.amazonaws.com/igv.org.genomes/rn7/rn7.genome rn7
Gorilla (Kamilah_GGO_v0/gorGor6) https://s3.amazonaws.com/igv.org.genomes/gorGor6/gorGor6.genome gorGor6

20 changes: 20 additions & 0 deletions genomes/sizes/129S1_SvImJ.chrom.sizes
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1 201072004
2 187098035
3 163015438
4 158993716
5 156226349
6 153203728
7 156033474
8 134068411
9 126413163
10 132218134
11 124783011
12 124738693
13 122598925
14 128831450
15 105959101
16 100461569
17 97444205
18 93001226
19 62815761
X 171044794
54 changes: 54 additions & 0 deletions genomes/sizes/2019-03-21_Creinhardtii_CC-503_v5.5.chrom.sizes
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chromosome_1 8033585
chromosome_2 9223677
chromosome_3 9219486
chromosome_4 4091191
chromosome_5 3500558
chromosome_6 9023763
chromosome_7 6421821
chromosome_8 5033832
chromosome_9 7956127
chromosome_10 6576019
chromosome_11 3826814
chromosome_12 9730733
chromosome_13 5206065
chromosome_14 4157777
chromosome_15 1922860
chromosome_16 7783580
chromosome_17 7188315
scaffold_18 271631
scaffold_19 219038
scaffold_20 200793
scaffold_21 189560
scaffold_22 163774
scaffold_23 127913
scaffold_24 127161
scaffold_25 102191
scaffold_26 80213
scaffold_27 55320
scaffold_28 55278
scaffold_29 52813
scaffold_30 52376
scaffold_31 48183
scaffold_32 42264
scaffold_33 39192
scaffold_34 33576
scaffold_35 32450
scaffold_36 25399
scaffold_37 24537
scaffold_38 24437
scaffold_39 22408
scaffold_40 22082
scaffold_41 21325
scaffold_42 21000
scaffold_43 20974
scaffold_44 17736
scaffold_45 16939
scaffold_46 16627
scaffold_47 14746
scaffold_48 14165
scaffold_49 13462
scaffold_50 12727
scaffold_51 11225
scaffold_52 6241
scaffold_53 2479
scaffold_54 2277
54 changes: 54 additions & 0 deletions genomes/sizes/2019-03-21_Creinhardtii_CC-503_v5.6.chrom.sizes
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chromosome_1 8033585
chromosome_2 9223677
chromosome_3 9219486
chromosome_4 4091191
chromosome_5 3500558
chromosome_6 9023763
chromosome_7 6421821
chromosome_8 5033832
chromosome_9 7956127
chromosome_10 6576019
chromosome_11 3826814
chromosome_12 9730733
chromosome_13 5206065
chromosome_14 4157777
chromosome_15 1922860
chromosome_16 7783580
chromosome_17 7188315
scaffold_18 271631
scaffold_19 219038
scaffold_20 200793
scaffold_21 189560
scaffold_22 163774
scaffold_23 127913
scaffold_24 127161
scaffold_25 102191
scaffold_26 80213
scaffold_27 55320
scaffold_28 55278
scaffold_29 52813
scaffold_30 52376
scaffold_31 48183
scaffold_32 42264
scaffold_33 39192
scaffold_34 33576
scaffold_35 32450
scaffold_36 25399
scaffold_37 24537
scaffold_38 24437
scaffold_39 22408
scaffold_40 22082
scaffold_41 21325
scaffold_42 21000
scaffold_43 20974
scaffold_44 17736
scaffold_45 16939
scaffold_46 16627
scaffold_47 14746
scaffold_48 14165
scaffold_49 13462
scaffold_50 12727
scaffold_51 11225
scaffold_52 6241
scaffold_53 2479
scaffold_54 2277
56 changes: 56 additions & 0 deletions genomes/sizes/2019-03-21_Creinhardtii_CC-503_v5.6_Cp+Mt_v4.4.chrom.sizes
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chromosome_1 8033585
chromosome_2 9223677
chromosome_3 9219486
chromosome_4 4091191
chromosome_5 3500558
chromosome_6 9023763
chromosome_7 6421821
chromosome_8 5033832
chromosome_9 7956127
chromosome_10 6576019
chromosome_11 3826814
chromosome_12 9730733
chromosome_13 5206065
chromosome_14 4157777
chromosome_15 1922860
chromosome_16 7783580
chromosome_17 7188315
scaffold_18 271631
scaffold_19 219038
scaffold_20 200793
scaffold_21 189560
scaffold_22 163774
scaffold_23 127913
scaffold_24 127161
scaffold_25 102191
scaffold_26 80213
scaffold_27 55320
scaffold_28 55278
scaffold_29 52813
scaffold_30 52376
scaffold_31 48183
scaffold_32 42264
scaffold_33 39192
scaffold_34 33576
scaffold_35 32450
scaffold_36 25399
scaffold_37 24537
scaffold_38 24437
scaffold_39 22408
scaffold_40 22082
scaffold_41 21325
scaffold_42 21000
scaffold_43 20974
scaffold_44 17736
scaffold_45 16939
scaffold_46 16627
scaffold_47 14746
scaffold_48 14165
scaffold_49 13462
scaffold_50 12727
scaffold_51 11225
scaffold_52 6241
scaffold_53 2479
scaffold_54 2277
Cp 205535
Mt 15789
6 changes: 6 additions & 0 deletions genomes/sizes/ASM294v2.chrom.sizes
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I 5579133
II 4539804
III 2452883
MT 19431
MTR 20128
AB325691 20000
1 change: 1 addition & 0 deletions genomes/sizes/ASM985889v3.chrom.sizes
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NC_045512.2 29903
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