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GT 11B Practice Velvet Assembly using Training Data

In order to become accustomed to the operation of GT, practice the mechanism and operation of assembly by Velvet using training sample data.

This BAM file is the assembly result of NGS lead by Velvet.

This operation is executable on GenomeTraveler.

Operation

Start GT.

Right-click the Velvet_assembling Node in the TREE pane.

The menu will be displayed.

Select Expand.

The velvet_assembling node is expanded.

Right-click on one Velvet-Assembling node.

The menu will be displayed.

Select Expand.

The node named kmer_21 / velvet_asm.afg is displayed.

Right click on the mouse on that node.

The menu will be displayed.

There is only one menu, select "Convert Afg to Bam".

This is a function to convert the afg format file which is the output file format of Velvet Assembler into the Bam format file which is the viewing file format in the alignment viewer.

A confirmation message will be displayed.

Click "Yes (Y)".

File conversion is executed.

A progress message is displayed during execution.

When finished, a completion message will be displayed.

Click "OK".

The node name is changed to kmer_21 / velvet_asm.bam.

Right-click on this node.

The menu will be displayed.

Select "Show Read Alignment".

A progress message is displayed during display processing.

The Alignment Viewer is displayed.

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