Difference between revisions of "Creosote"
From CoGepedia
(20 intermediate revisions by the same user not shown) | |||
Line 1: | Line 1: | ||
− | + | ==Twig2Genome Notes== | |
+ | [[Twig2Genome]] | ||
− | + | ==Assembly== | |
− | + | [[Creosote Assembly]] | |
− | + | ||
− | + | ==Loading into CoGe== | |
− | + | SoapDeNovo assemly: 1,570,116 contigs (370MB): http://genomevolution.org/CoGe/OrganismView.pl?dsgid=12183 ('''Note:''' too many contigs to process and visualize in SynMap) | |
− | + | ||
− | + | SoapDeNovo assembly of contigs >= 2000nt: 6,976 contigs (20MB): http://genomevolution.org/CoGe/OrganismView.pl?dsgid=12185 | |
− | + | ||
− | + | ABySS assembly (bpsize=64, 2kb minimum contig size): 122,972 contigs (392MB): http://genomevolution.org/CoGe/OrganismView.pl?dsgid=12275 | |
− | * | + | *Syntenic Path Assembly to peach: http://genomevolution.org/r/3xmq |
− | * | + | |
− | + | Velvet assembly 515,190 contigs (241MB): http://genomevolution.org/CoGe/OrganismView.pl?dsgid=12245 | |
− | + | ||
− | + | CLC4 assembly 685,475 contigs (508MB): http://genomevolution.org/CoGe/OrganismView.pl?dsgid=12244 | |
− | + | *Syntenic Path Assembly to peach: http://genomevolution.org/r/3xpd | |
− | + | ||
− | + | ==[[Syntenic Path Assembly]]== | |
− | + | ||
− | + | [[File:Master 12185 8400.genomic-CDS.lastz.dag.go c20 D20 g10 A2.aligncoords.gcoords ct0.w1000.ass2.cs1.csoS.nsd.png|thumb|600px|left|Syntenic path assembly with SynMap of creosote (x-axis) and peach (y-axis). Results may be regenerated at: http://genomevolution.org/r/3w95]] | |
− | + | ||
− | + | [[File:Master 11022 12185.CDS-genomic.lastz.dag.go c20 D20 g10 A2.aligncoords.gcoords ct0.w1000.ass2.cs1.csoS.nsd.png|thumb|600px|left|Syntenic path assembly with SynMap of creosote (y-axis) and Arabidopsis thaliana Col-0 (x-axis). Results may be regenerated at: http://genomevolution.org/r/3w96]] | |
− | + | ||
− | + | ==Pseudo-Assembly== | |
+ | [[File:Pseudo-assembly-creosote.png|thumb|600px|left|Pseudo-assembly of creosote (x-axis) using the peach (y-axis) genome. Syntenic comparison to the peach genome.]] | ||
+ | |||
+ | [[File:Screen Shot 2014-05-14 at 8.33.27 AM.png|thumb|600px|left|Microsynteny analysis of the pseudo-assembled creosote genome to the peach genome. Orange bars are unsequenced Ns that represent contigs glued together in creosote by the [[syntenic path assembly]] method. Note the concordance of gene model coding sequences.]] |
Latest revision as of 07:35, 14 May 2014
Contents
Twig2Genome Notes
Assembly
Loading into CoGe
SoapDeNovo assemly: 1,570,116 contigs (370MB): http://genomevolution.org/CoGe/OrganismView.pl?dsgid=12183 (Note: too many contigs to process and visualize in SynMap)
SoapDeNovo assembly of contigs >= 2000nt: 6,976 contigs (20MB): http://genomevolution.org/CoGe/OrganismView.pl?dsgid=12185
ABySS assembly (bpsize=64, 2kb minimum contig size): 122,972 contigs (392MB): http://genomevolution.org/CoGe/OrganismView.pl?dsgid=12275
- Syntenic Path Assembly to peach: http://genomevolution.org/r/3xmq
Velvet assembly 515,190 contigs (241MB): http://genomevolution.org/CoGe/OrganismView.pl?dsgid=12245
CLC4 assembly 685,475 contigs (508MB): http://genomevolution.org/CoGe/OrganismView.pl?dsgid=12244
- Syntenic Path Assembly to peach: http://genomevolution.org/r/3xpd