Can the Geneious assembler do scaffolding?

From R8 onwards, the Geneious de novo assembler can be configured to produce scaffolds where contigs are linked by paired read information.  The missing region between contigs is filled by Ns.  To enable this option, you must first pair your reads by running “Set paired reads” under the “Sequence” menu.  Then go to De novo assemble, click More Options and check “Produce Scaffolds”.

Have more questions? Submit a request


  • Avatar
    Travis Glenn

    I am trying to assemble a fungal genome (~50M), which may be possible to do in Geneious.  For sure Geneious is really nice for letting me trim the data.  Everything is going well for quality & adapter trimming both short-insert genomic data as well as Nextera Mate-Pair data, until I get to the internal adapter stage on the Nextera Mate-Pairs.  I can find the internal adapters (and thus which sequences have them), but I haven't figured out how to extract only the sequences that have these internal adapters.  

    I would like to 1) find all sequences that have the internal adapters, 2) extract all sequences that have the internal adapters, and then 3) trim the adapters off (but only from the sequences in group 2).

    I know how to do 1 & 3, but not #2.  If I use Trim Ends, that gets rid of the internal adapters, but I haven't filtered out the read pairs that don't have the adapter.  It would be great to know how to do this.  It would also be great to know if there were assembly programs in Geneious that could use the internal read adapter information automagically (without needing to trim it).


  • Avatar
    Hilary Miller

    To extract all sequences that have a specific, internal adaptor sequence the easiest way is to annotate the adapter sequence on the read, and then use "Extract Annotations" under the Tools menu to pull out the reads with the annotation.  In Extract Annotations choose "Entire sequence" under "What to extract" and it will pull the entire read out, not just the annotated sequence.  

    You might be able to do the extraction using the "trimmed" annotation that you got from running trim ends.  Otherwise, you can search for and annotate the adapter sequence as follows:

    1. Search for motifs (under Annotate and Predict)- this is really slow on large datasets but will search for and annotate a specific motif.

    or 2.  Find in Document (under Edit) - Choose "Find all", and it will select all the instances of your motif in your dataset.  Then choose "Add Annotation" to add a motif annotation to all the selected sequences.  You'll need a reasonable amount of RAM to do this as it has to load the entire document into memory.