Viewing Contigs with the Alignment Results Tab

1.10	Viewing Contigs with the Alignment Results Tab

Click on the Alignment Results tab to view the alignment data from the assembly computation (Figure 20). This tab shows the contigs and their underlying multiple alignments.

Consensus sequence supported by a single read is considered unreliable. Regions of the assembly covered by only a single read are excluded from the assembly results. This exclusion could possibly result in contig shrinkage or breakage.

Figure 20: gsAssembler Alignment Results Tab

The left panel of the Alignment Results tab contains a list of the contigs produced by the assembly project. By default, the first contig on the list will be automatically selected.

The multi-alignment panel has the following features:

•	The larger area, on white background, contains the multiple alignment proper

•	The selected contig consensus sequence is shown on top of the panel, gapped for insertions in the aligned reads

•	The reads underlying the contig’s multiple alignment, gapped and showing bases that diverge from the consensus as red dashes on yellow background

•	The names of the contig and reads in the multiple alignment appear in a column, on the left side of the multiple alignment area

•	Scroll bars allow you to navigate the alignment manually:

•	Clicking on the arrowheads on either side of a scroll bar scrolls the alignment by one base (horizontal) or one read (vertical) in the direction of the arrowhead

•	Clicking on the light-colored area on either side of the horizontal scroll bar “handle” scrolls the alignment by 40 bases is the corresponding direction

•	Clicking and dragging the “handle” of a scroll bar allows you to move larger distances rapidly

•	Right clicking on a GS read will produce a “Get flowgram for … at selected position” menu item which, if selected, will activate the Flowgrams tab and display the flowgram for the read; centered on the flow corresponding to the base on which the user clicked to activate the option.

This capability is not active for FASTA/FASTQ reads or the contig/consensus sequences themselves, for which no flowgrams are available.

•	Above that area are some informational and navigational controls:

◦	Go To: A data entry field and a Go To button allow you to navigate directly to a position of interest: enter a number not larger than the length of the selected contig in the data entry field, and click the Go To button.

◦	A ‘zoom to selected’ button can be used to zoom in, centering on the selected base. If no base is selected, it will use the base in the center of the current view as a default.

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The zoom-slider tool allows for more or fewer bases to be viewed at a time in the main window. If the slider is set to all the way zoom out (-) then the individual bases are grayed out but the shape of the read alignment is still shown along with the positions of the differences highlighted in yellow (Figure 21).

◦	Camera icon: saves an image of the part of the multiple alignment table currently visible on screen, to a file in .png format.

•	The Alignment Results tab also features a “Mouse Tracker” area, in the left panel, below the list of contig sequences. If you pause the mouse pointer over a base in the multi-alignment, the following information is provided about that base:

◦	Base: the position of that base relative to the selected contig sequence; gaps in the contig sequence are displayed as the following base of the contig

◦	Read: the name of the read or contig to which this base belongs

◦	Val: the “value” of the base under the mouse pointer, in that read, i.e. A, G, T, C

Figure 21: gsAssembler Alignment Results tab with the zoom slider all the way out