Difference between revisions of "XENLA Genome"
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= Genome version = | = Genome version = | ||
+ | In here, 'N50' is calculated based on the combination of 'Scaffolds' and 'Contigs', so it may be slightly different to official report of 'Scaffolds N50'. | ||
+ | |||
+ | Sequences 'in public' are available at ftp://ftp.xenbase.org/pub/Genomics/JGI/ | ||
+ | |||
{| class="wikitable" style="text-align: center" width=800 | {| class="wikitable" style="text-align: center" width=800 | ||
!Name | !Name | ||
Line 84: | Line 88: | ||
|1.15 Mbp | |1.15 Mbp | ||
|5,714 | |5,714 | ||
− | |JGI7; | + | |JGI7;Released in public. |
|- | |- | ||
|JGIv7b | |JGIv7b | ||
Line 91: | Line 95: | ||
|3.49 Mbp | |3.49 Mbp | ||
|2,598 | |2,598 | ||
− | |JGI7. | + | |JGI7.1;Released in public. Minor updates of 7.0. |
|} | |} | ||
− | = Data Summary = | + | = J-strain Genomic Data Summary = |
== Whole genome shotgun sequencing, JGI/UC Berkeley, USA == | == Whole genome shotgun sequencing, JGI/UC Berkeley, USA == | ||
− | * Illumina mate-pair | + | === J strain === |
+ | * JBL_009 Illumina paired-end (225 bp insertion), 2x150: 320 M reads, 48 G bases | ||
+ | * JBL_010 Illumina paired-end (450 bp insertion), 2x150: 264 M reads, 40 G bases | ||
+ | * JBL_011 Illumina paired-end (900 bp insertion), 2x150: 424 M reads, 64 G bases | ||
+ | * JBL_012 Illumina mate-pair (1,500 bp insertion), 2x100: 320 M reads, 32 G bases | ||
+ | * JBL_013 Illumina mate-pair (4,000 bp insertion), 2x100: 328 M reads, 33 G bases | ||
+ | |||
+ | === F strain === | ||
+ | * JBL_005 Illumina paired-end, 2x100: 416 M reads, 42 G bases | ||
+ | * JBL_005b Illumina paired-end, 2x150: 464 M reads, 70 G bases | ||
+ | |||
+ | === F/J hybrid === | ||
+ | * JBL_007 Illumina paired-end, 2x150: 344 M reads, 52 G bases | ||
== Whole genome shotgun sequencing, NIG/U Tokyo, Japan == | == Whole genome shotgun sequencing, NIG/U Tokyo, Japan == | ||
+ | === J strain === | ||
* Illumina paired-end (207 bp insertion): 1,004 M reads, 105 G bases | * Illumina paired-end (207 bp insertion): 1,004 M reads, 105 G bases | ||
* Illumina paired-end (425 bp insertion): 672 M reads, 78 G bases | * Illumina paired-end (425 bp insertion): 672 M reads, 78 G bases | ||
Line 108: | Line 125: | ||
== Whole genome shotgun sequencing, UT Austin, USA == | == Whole genome shotgun sequencing, UT Austin, USA == | ||
− | * SOLiD mate-pair | + | * SOLiD v3 mate-pair (1,500 bp insertion): 608 M reads, 30 G bases |
− | == | + | == Fosmid-end sequencing, JGI/Berkeley + UW, USA == |
− | * Illumina | + | * Illumina paired-end (? bp insertion): 18 M reads, 1.35 G bases |
== BAC-end sequencing, NIG/U Tokyo, Japan == | == BAC-end sequencing, NIG/U Tokyo, Japan == | ||
* Sanger sequencing | * Sanger sequencing | ||
+ | * SceI BACs: 720,384 sequences in total. 458,392 sequences with good pairs (233 k pairs; mean length 1,061 bp) | ||
+ | * HindIII BACs: 38,400 sequences in total. 34,044 sequences with good pairs (17 k pairs; mean length 1,125 bp) | ||
− | == | + | == Fosmid-end sequencing, NIG/U Tokyo, Japan == |
* Sanger sequencing | * Sanger sequencing | ||
+ | * 119,808 sequences in total. 99,652 sequences with good pairs (50 k pairs; mean length 1,106 bp). | ||
+ | |||
+ | == BAC full sequencing, NIG/U Tokyo, Japan == | ||
+ | * Sanger sequencing. | ||
+ | * 30 BACs (mean length 112 kb). | ||
+ | |||
+ | == Fosmid shotgun sequencing, JGI/Berkeley + UW, USA == | ||
+ | * Illumina single-end: 102 M reads, 3.5 G bases | ||
== BAC shotgun sequencing, UT Austin, USA == | == BAC shotgun sequencing, UT Austin, USA == | ||
− | * One plate of CHORI-210 (96 BACs). | + | * One plate of CHORI-210 (96 BACs). |
+ | * SOLiD v3 mate-pair (2,000 bp insertion): 70 M reads, 3.5 G bases | ||
+ | * SOLiD v3 mate-pair (5,000 bp insertion): 56 M reads, 2.8 G bases | ||
== FISH, NIG/U Tokyo, Japan == | == FISH, NIG/U Tokyo, Japan == | ||
+ | = See Also = | ||
+ | [[XENLA_Transcriptome]], [[XENLA_Proteome]] | ||
---- | ---- | ||
[[Category:XenopusGenome]] | [[Category:XenopusGenome]] |
Latest revision as of 11:30, 8 May 2014
Genome browser
- XenBase - JGIv6
- NIMR, UK (Mike Gilchrist) - JGIv5(2011oct), JGIv6a(2012nov)
- NIG, Japan (Asao Fujiyama & Masanori Taira) - NIGv2
Genome version
In here, 'N50' is calculated based on the combination of 'Scaffolds' and 'Contigs', so it may be slightly different to official report of 'Scaffolds N50'.
Sequences 'in public' are available at ftp://ftp.xenbase.org/pub/Genomics/JGI/
Name | Release Date | Concat. Length (bp) | N50 (bp) | Scaffolds > 10kbp | Remarks |
---|---|---|---|---|---|
JGIv1 | 2010 Dec. | 2.30 Gbp | 8 kbp | 385,933 | Internal Use Only. |
JGIv5 | 2011 Oct. | 2.84 Gbp | 0.28 Mbp | 16,625 | Released in Xenopus PI Meeting. |
JGIv6 | 2012 Jul. | 2.75 Gbp | 0.70 Mbp | 8,426 | Officially released in XenBase. |
JGIv6a | 2012 Jul. | 2.75 Gbp | 0.70 Mbp | 8,426 | Officially released in XenBase; Minor update of JGIv6. |
NIGv1 | 2012 Nov. | 2.88 Gbp | 0.34 Mbp | 14,260 | Original name is 'xl.v1soap'; Internal Use Only. |
NIGv1ap | 2012 Nov. | 3.27 Gbp | 0.17 Mbp | 39,283 | Original name is 'xl.v3ap'(AllPath?); Internal Use Only. |
NIGv1m | 2012 Nov. | 2.84 Gbp | 0.28 Mbp | 82,132 | Original name is 'xl.v5m'; Internal Use Only. |
NIGv2 | 2013 Feb. | 2.89 Gbp | 0.72 Mbp | 5,394 | Original name is 'xl.v2soap'; Internal Use Only. |
NIGv2c | 2013 Feb. | 2.88 Gbp | 0.71 Mbp | 5,377 | Original name is 'xl.v2soap,GapClosed'; Can browse at NIG gbrowser. |
JGIv7a | 2013 Mar. | 2.72 Gbp | 1.15 Mbp | 5,714 | JGI7;Released in public. |
JGIv7b | 2013 May | 2.78 Gbp | 3.49 Mbp | 2,598 | JGI7.1;Released in public. Minor updates of 7.0. |
J-strain Genomic Data Summary
Whole genome shotgun sequencing, JGI/UC Berkeley, USA
J strain
- JBL_009 Illumina paired-end (225 bp insertion), 2x150: 320 M reads, 48 G bases
- JBL_010 Illumina paired-end (450 bp insertion), 2x150: 264 M reads, 40 G bases
- JBL_011 Illumina paired-end (900 bp insertion), 2x150: 424 M reads, 64 G bases
- JBL_012 Illumina mate-pair (1,500 bp insertion), 2x100: 320 M reads, 32 G bases
- JBL_013 Illumina mate-pair (4,000 bp insertion), 2x100: 328 M reads, 33 G bases
F strain
- JBL_005 Illumina paired-end, 2x100: 416 M reads, 42 G bases
- JBL_005b Illumina paired-end, 2x150: 464 M reads, 70 G bases
F/J hybrid
- JBL_007 Illumina paired-end, 2x150: 344 M reads, 52 G bases
Whole genome shotgun sequencing, NIG/U Tokyo, Japan
J strain
- Illumina paired-end (207 bp insertion): 1,004 M reads, 105 G bases
- Illumina paired-end (425 bp insertion): 672 M reads, 78 G bases
- Illumina paired-end (900 bp insertion): 695 M reads, 60 G bases
- Illumina mate-pair (1,387 bp insertion): 188 M reads, 15 G bases
- Illumina mate-pair (3,762 bp insertion): 188 M reads, 15 G bases
- Illumina mate-pair (9,850 bp insertion): 239 M reads, 18 G bases
Whole genome shotgun sequencing, UT Austin, USA
- SOLiD v3 mate-pair (1,500 bp insertion): 608 M reads, 30 G bases
Fosmid-end sequencing, JGI/Berkeley + UW, USA
- Illumina paired-end (? bp insertion): 18 M reads, 1.35 G bases
BAC-end sequencing, NIG/U Tokyo, Japan
- Sanger sequencing
- SceI BACs: 720,384 sequences in total. 458,392 sequences with good pairs (233 k pairs; mean length 1,061 bp)
- HindIII BACs: 38,400 sequences in total. 34,044 sequences with good pairs (17 k pairs; mean length 1,125 bp)
Fosmid-end sequencing, NIG/U Tokyo, Japan
- Sanger sequencing
- 119,808 sequences in total. 99,652 sequences with good pairs (50 k pairs; mean length 1,106 bp).
BAC full sequencing, NIG/U Tokyo, Japan
- Sanger sequencing.
- 30 BACs (mean length 112 kb).
Fosmid shotgun sequencing, JGI/Berkeley + UW, USA
- Illumina single-end: 102 M reads, 3.5 G bases
BAC shotgun sequencing, UT Austin, USA
- One plate of CHORI-210 (96 BACs).
- SOLiD v3 mate-pair (2,000 bp insertion): 70 M reads, 3.5 G bases
- SOLiD v3 mate-pair (5,000 bp insertion): 56 M reads, 2.8 G bases
FISH, NIG/U Tokyo, Japan
See Also
XENLA_Transcriptome, XENLA_Proteome