10.5 Viewing Contigs

Contigs in Geneious Prime are viewed (and edited) in exactly the same way as alignments. There are several features in the sequence viewer which are worth taking special note of when viewing contigs:


Figure 10.6: The overview of a contig

    Finding regions of low/high coverage
    Viewing Contigs of Paired Reads
Finding regions of low/high coverage

In addition to the coverage graph which gives you a quick overview of coverage, under the Annotate & Predict toolbar is the Find Low/High Coverage feature. This feature annotates all regions of low/high coverage which you can then navigate through using the little left and right arrows next to the coverage annotations in the controls on the right. You can set the threshold low/high coverage by either specifying an absolute number of sequences or a number of standard deviations from the mean coverage.

The find low/high coverage tool can also be used to record the minimum, mean, and maximum coverage of each annotation of a particular type on the reference sequence. To do this, in the Only Find In section of the options, turn on Annotations in reference sequence of type and choose Create annotations of same type on reference sequence.

Viewing Contigs of Paired Reads

In order to view a contig of paired reads, you first need to have set up the paired data before assembling - see 10.2.1 . Once you have your paired read assembly, the contig viewer adds an option to Link paired reads in the advanced section of the controls on the right. This means that pairs of reads will be laid out in the same row with a horizontal line connecting them. Reads separated by more than 3 times their expected distance are not linked by default unless the Link distant reads setting is turned on.

The horizontal line between paired reads is colored according to how close the separation between the reads is to their expected separation. Green indicates they are correct, yellow and blue indicate under or over their expected separation and red indicates the reads are incorrectly orientated.

The reads themselves can also be configured to be colored in this way if you use the Paired Distance color scheme from the general (top section in the controls on the right) settings. The colors used and the sensitivity for deciding if reads are close enough to their expected distance can be configured from the Options link when the Paired Distance color scheme is selected.

You can hover the mouse of any read in a contig and the status bar will indicate the expect separation and expected separation between the reads.