Syntenic path assembly: Difference between revisions

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==Overview==
The Syntenic Path Assembly is an option in [[SynMap]] to do a reference genome assembly of contigs using synteny to determine the order and orientation of the contigs.  To use this option, select "Order contigs by best syntenic path" under the Display Options tab.
[[Image:Screen shot 2011-02-18 at 1.38.59 PM.png|thumb|500px|center|Selecting the Syntenic Path Assembly option in [[SynMap]]]]
[[Image:Screen shot 2011-02-18 at 1.58.23 PM.png|frame|center|running a syntenic path assembly in SynMap, there is an option to download the assembled sequence (contigs are joined using 100Ns).]]
==E. coli==
<gallery widths=500px heights=500px caption="Syntenic Path Assembly in SynMap of E. coli">
<gallery widths=500px heights=500px caption="Syntenic Path Assembly in SynMap of E. coli">
File:Screen shot 2011-02-18 at 1.24.54 PM.png|[[SynMap]] analysis of a WGS assembly of a strain of E. coli K12 (y-axis) to a reference assembly (x-axis).  Results may be regenerated at http://genomevolution.org/r/2k70
File:Screen shot 2011-02-18 at 1.24.54 PM.png|[[SynMap]] analysis of a WGS assembly of a strain of E. coli K12 (y-axis) to a reference assembly (x-axis).  Results may be regenerated at http://genomevolution.org/r/2k70
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</gallery>
</gallery>


The Syntenic Path Assembly is an option in [[SynMap]] to do a reference genome assembly of contigs using synteny to determine the order and orientation of the contigs.  To use this option, select "Order contigs by best syntenic path" under the Display Options tab.
[[Image:Screen shot 2011-02-18 at 1.38.59 PM.png|thumb|500px|center|Selecting the Syntenic Path Assembly option in [[SynMap]]]]


==Puffer fish:  Takifugu rubripes and Tetraodon nigroviridis==
<gallery widths =500px heights=500px compation="Syntenic Path Assembly in SynMap of distally related puffer fish">
<gallery widths =500px heights=500px compation="Syntenic Path Assembly in SynMap of distally related puffer fish">
File:Screen shot 2011-02-18 at 1.52.19 PM.png|Syntenic dotplot using [[SynMap]] between two puffer fish, Takifugu rubripes (x-axis) and Tetraodon nigroviridis (y-axis). Fugu is a WGS assembly. Results may be regenerated at http://genomevolution.org/r/2k7b
File:Screen shot 2011-02-18 at 1.52.19 PM.png|Syntenic dotplot using [[SynMap]] between two puffer fish, Takifugu rubripes (x-axis) and Tetraodon nigroviridis (y-axis). Fugu is a WGS assembly. Results may be regenerated at http://genomevolution.org/r/2k7b
File:Screen shot 2011-02-18 at 1.41.51 PM.png|Syntneic dotplot using [[SynMap]] between two puffer fish, Takifugu rubripes (x-axis) and Tetraodon nigroviridis (y-axis) using the Syntenic Path Assembly option. Fugu is a WGS assembly and fully syntenic converage to Tetraodon is detectable. Results may be regenerated at http://genomevolution.org/r/2k79
File:Screen shot 2011-02-18 at 1.41.51 PM.png|Syntneic dotplot using [[SynMap]] between two puffer fish, Takifugu rubripes (x-axis) and Tetraodon nigroviridis (y-axis) using the Syntenic Path Assembly option. Fugu is a WGS assembly and fully syntenic converage to Tetraodon is detectable. Results may be regenerated at http://genomevolution.org/r/2k79
</gallery>
</gallery>
[[Image:Screen shot 2011-02-18 at 1.58.23 PM.png|frame|center|running a syntenic path assembly in SynMap, there is an option to download the assembled sequence (contigs are joined using 100Ns).]]

Revision as of 00:37, 20 February 2011

Overview

The Syntenic Path Assembly is an option in SynMap to do a reference genome assembly of contigs using synteny to determine the order and orientation of the contigs. To use this option, select "Order contigs by best syntenic path" under the Display Options tab.

Selecting the Syntenic Path Assembly option in SynMap
running a syntenic path assembly in SynMap, there is an option to download the assembled sequence (contigs are joined using 100Ns).


E. coli

  • Syntenic Path Assembly in SynMap of E. coli
  • SynMap analysis of a WGS assembly of a strain of E. coli K12 (y-axis) to a reference assembly (x-axis). Results may be regenerated at http://genomevolution.org/r/2k70
    SynMap analysis of a WGS assembly of a strain of E. coli K12 (y-axis) to a reference assembly (x-axis). Results may be regenerated at http://genomevolution.org/r/2k70
  • SynMap analysis of a WGS assembly of a strain of E. coli K12 (y-axis) to a reference assembly (x-axis) using SynMap's Syntenic Path Assembly to order contigs. Results may be regenerated at: http://genomevolution.org/r/2k71
    SynMap analysis of a WGS assembly of a strain of E. coli K12 (y-axis) to a reference assembly (x-axis) using SynMap's Syntenic Path Assembly to order contigs. Results may be regenerated at: http://genomevolution.org/r/2k71


Puffer fish: Takifugu rubripes and Tetraodon nigroviridis

  • Syntenic dotplot using SynMap between two puffer fish, Takifugu rubripes (x-axis) and Tetraodon nigroviridis (y-axis). Fugu is a WGS assembly. Results may be regenerated at http://genomevolution.org/r/2k7b
    Syntenic dotplot using SynMap between two puffer fish, Takifugu rubripes (x-axis) and Tetraodon nigroviridis (y-axis). Fugu is a WGS assembly. Results may be regenerated at http://genomevolution.org/r/2k7b
  • Syntneic dotplot using SynMap between two puffer fish, Takifugu rubripes (x-axis) and Tetraodon nigroviridis (y-axis) using the Syntenic Path Assembly option. Fugu is a WGS assembly and fully syntenic converage to Tetraodon is detectable. Results may be regenerated at http://genomevolution.org/r/2k79
    Syntneic dotplot using SynMap between two puffer fish, Takifugu rubripes (x-axis) and Tetraodon nigroviridis (y-axis) using the Syntenic Path Assembly option. Fugu is a WGS assembly and fully syntenic converage to Tetraodon is detectable. Results may be regenerated at http://genomevolution.org/r/2k79
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