Creosote

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

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

Pseudo-assembly of creosote (x-axis) using the peach (y-axis) genome. Syntenic comparison to the peach genome.

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.