General

Contig Editor with a pre-assembled contig without read data

Contig Editor with a pre-assembled next-gen contig with read data imported from an ACE file

Contig Editor with a contig assembled from two chromatograms

The Contig Editor consists of different panels that can be shown or hidden with buttons on the right border. In the Task Template it can be defined which panels are shown by default.

The following panels are available:

Contig Overview: For viewing a bird's eye view of the whole contig alignment. This feature is only available for Sanger sequencing data.

Ref.-seq. Alignment: For viewing and modifying the alignment between consensus and RefSeq.

Contig: For viewing and editing the consensus or the reads. Use right-click or keyboard shortcuts for base editing.

Reads: For viewing and editing the reads of the contig. Use right-click or keyboard shortcuts for base editing. This feature is only available for Sanger sequencing data.

Variants: For viewing and controlling all variants that were found between consensus and RefSeq.

Analysis: For viewing the analysis warnings and messages for this target.

The three panels that show DNA sequences (Ref.-seq., Contig, and Reads) have a cyan colored cursor that marks current position in the sequence. The button can be used to link the sequence panels to each other: Placing the cursor in one of them synchronizes the cursor of all other editor panels to the corresponding position.

Contig Overview Panel

A bird's eye view showing the alignment between the ref.-seq., the consensus, and the reads. This feature is only available for Sanger sequencing data.

Ref.-seq. Alignment Panel

If a Reference sequence was defined, this panel shows the alignment between the consensus and the Reference sequence base by base, and below the translation to amino acids according to the Ref.-seq. layer information.

The toolbar above the sequences shows the following actions:

Jump to next marked position left
Jump to next marked position right
Show/Hide the marks of translation differences between RefSeq and contig
Show/Hide the marks for SNPs (single nucleotide polymorphisms) between RefSeq and contig
Show/Hide the marks for MNPs (multiple nucleotide polymorphisms) between RefSeq and contig
Show/Hide the marks for DPs (deletion polymorphisms) between RefSeq and contig
Show/Hide the marks for IPs (insertion polymorphisms) between RefSeq and contig
Allows to filter the polymorphism marks (SNP/MNP/DP/IP) that are shown:
- Only show unknown variants (=not defined in the Task Template)
- Only show known variants (=defined in the Task Template)
- Only show known variants that are used for result fields
Find a short base sequence in the RefSeq, the result is shown as yellow find marks in the sequence
Remove find marks
Summarized information and statistics about the alignment
Show/Hide the amino acid translations
Search for stop codons in the sequence to predict the frame offset
Show the reference sequence parameters for this target
The Reference sequence alignment is calculated dynamically, updated each time the contig is modified. By pressing the button Alignment Ref.-seq. Editing, the current Ref.-seq. alignment can be "frozen", and the gaps inserted or deleted manually using the right-click menu. They can also be moved by dragging the gap with the mouse. Press the button again to discard all editing in the Ref.-seq. alignment and recalculate it.

Right-click on a position in the sequence to access further actions in context menu:

Insert Gap: Insert a gap the selected row, left of the currently selected position (only available if the button for Ref.-seq. Alignment Editing was pressed)
Remove Gap: Remove the gap on the selected position (only available if the button for Ref.-seq. Alignment Editing was pressed).
Remove Gap Column: Remove a column in the alignment that contains only gap (only available if the button for Ref.-seq. Alignment Editing was pressed).

Matching Style: Changes the visual marking of matching and mismatching bases in the contig alignment.
Amino Acid Style: Switch between single letter and three letter names for the translated amino acids.

Copy Selection: Copy the currently selected bases of a row to the clipboard.

Copy Sequence: Copy a complete sequence row to clipboard.

Export Alignment to File: Export Ref.-seq. alignment to a file.

Editor Preferences: Show some settings for the visual appearance of this view.

Contig Panel

Showing the Contig with the consensus and the assembled reads bases.

The toolbar above the sequences shows the following actions:

Reassemble the reads of this target. This feature is only available for Sanger sequencing data.
Undo last editing
Redo last undone editing
Crop the contig left of the current position
Crop the contig right of the current position
Reset the contig cropping the default defined by the Task Template
Jump to next marked position left
Jump to next marked position right
Show/Hide marks for the found signatures, as defined in the Task Template
Show/Hide marks for the ambiguity bases
Show/Hide marks for the low quality bases, as defined in the Task Template Analysis
Set/Unset a user defined mark
Show/Hide marks for all mismatches in the read alignment
Show/Hide marks for all gaps in the read alignment
Find a short base sequence in the consensus, the result is shown as yellow find marks in the sequence
Remove find marks
Summarized information and statistics about the contig. If the read alignments are available for the contig, the per base read coverage is also shown.

Right-click on a position to access further actions in context menu:

Substitute all Read Bases: Replace all read bases for the currently selected consensus base and update the consensus base.
Keyboard shortcut: A, C, G, T or an ambiguity symbol
This feature is only available for Sanger sequencing data.
Delete all Read Bases: Delete all read bases for the currently selected consensus base and update the consensus base.
Keyboard shortcut: insert
This feature is only available for Sanger sequencing data.
Insert all Read Bases: Insert a new base in all read bases left of the currently selected position and update the consensus base.
Keyboard shortcut: delete
This feature is only available for Sanger sequencing data.

Substitute Consensus Base: Replace the currently selected consensus base.
Keyboard shortcut: A, C, G, T or an ambiguity symbol
This feature is only available for whole genome sequencing data.
Delete Consensus Base: Delete the currently selected consensus base.
Keyboard shortcut: insert
This feature is only available for whole genome sequencing data.
Insert Consensus Base: Insert a new base in the consensus left of the currently selected position.
Keyboard shortcut: delete
This feature is only available for whole genome sequencing data.

Insert Gap: Insert a gap in a read row of the contig alignment, left of the currently selected position.
Remove Gap: Remove a gap in a read row of the contig alignment.

Reverse complement: Convert the contig to its reverse complement.

Matching Style: Changes the visual marking of matching and mismatching bases in the contig alignment
Show Base Qualities: Show/Hide the consensus qualities.

Copy Selection to Clipboard: Copy the currently selected bases of the consensus to the clipboard.

Copy Selection and Aligned Bases to Clipboard: Copy the currently selected bases of the consensus and all the read of this region to the clipboard (FASTA format).

Copy Consensus Area(s) to Clipboard: Copy all consensus bases to clipboard, that covered by an area in the aligned RefSeq.

Export Consensus Area(s) to File: Export all consensus bases to a FASTA file, that covered by an area in the aligned RefSeq.

Info: Shows a summary about the contig alignment.

Editor Preferences: Show some settings for the visual appearance of the contig editor.

Reads Panel

This panels show the read sequences (e.g. chromatograms) that were used in the contig alignment. This feature is only available for Sanger sequencing data.

The toolbar above the reads shows the following buttons:

Normalize the base call distance of all chromatogram peaks
By default the read view is automatically arranged in columns and rows, can be changed with this drop down button
Zoom in vertically
Set vertical scale to default
Zoom out vertically
Slider: Adjust the horizontal scale
open this panel in a new window
close this panel

Variants Panel

Showing all variant position that appear between the RefSeq and the consensus.

Go to previous row in table and set the focus in the contig to the according base position
Go to next row in table and set the focus in the contig to the according base position
Export the table to a file
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close this panel

The table contains the following columns:

VQ: Variant Quality, may be (good) or (bad) according to the settings in the Task Template

Variant: Type of variant: SNP (single nucleotide polymorphism), IP (insertion p.), DP (deletion p.), or MNP (multiple n. p.)

Position: Base Position in the RefSeq

Abs. Position: Base position in the whole genome, if the RefSeq was extracted from an annotated genome

Area Position: Base position in the area in which this variant occurs

Length: Length of this variant, SNPs have always length 1

Base Change: The base change produced by this variant shown as Variant Base(s) : Reference Base(s)

AA Change: The amino acid change produced by this variant shown as Variant AA : Reference AA

Codon Number: The number of the codon to which the variant base belongs to, if the area is translatable

BQ: The base quality/ies of the variant base(s)

Area: The area in which the variant occurs

Known Variant: shows the known variants, if any are defined for this position and area

Codon Effect: Shows the translation effect for the reference codon and the contig codon of the variant

SNP Effect: Shows the translation effect for the reference codon and the modified reference codon with the variant

Var. Codon: The codon in the contig

Ref. Codon: The codon in the reference sequence

Var. Pos. i.c.: The position of the variant in the codon, may be 1, 2 or 3

Analysis Panel

Showing the result of the Target Analysis as it is defined in the Target Parameters of the Task Template.

Go to previous row in table and set the focus in the contig to the according base position
Go to next row in table and set the focus in the contig to the according base position
Ignore selected errors. If allowed by the Task Template's analysis settings, specific analysis errors may be ignored.
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