Difference between revisions of "Creosote"
From CoGepedia
(Created page with 'Creosote genome sequencing and assembly notes: *Sample obtained from front yard of 4951 W. McElroy Dr. *Sequences obtained from one lane of Illumina HiSeq2000 *Fastq files deliv...') |
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| − | + | ==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
Syntenic Path Assembly
Syntenic path assembly with SynMap of creosote (x-axis) and peach (y-axis). Results may be regenerated at: http://genomevolution.org/r/3w95
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
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.
