Geneious workflow to grow contigs` extremities

Fabs Labs

• March 22, 2019 02:09

Hello, I could use some help.

I would like a Grow Contigs Workflow that does a Map to Reference to a linear contig that generates a consensus sequence and then it follows up with a new Map to Reference using the consensus of the last as the reference and the reads of the first again (or the unused reads of the first), this would go on ad infinitum or a predetermined number of times.

Before anyone says that increasing iterations of a Map to Reference would do that, it doesn`t work like that at all, although it says it would. An assembly may do that but it takes too long without guidance.

I have tried to generate a workflow using the workflow wizard, but after the first mapping it fails to automatically detect a reference sequence for the second mapping. I have little knowledge of Java coding to be able to program it, although it seems simple enough.

 

Thanks!

0

• 

  Moreland Gibbs

  • March 25, 2019 00:44

  Hi,

  I am not sure what you are suggesting will be faster or better that the current Iterate function.

  Increasing the Geneious Prime mapper "Iterations" setting should "grow" your assembly beyond the bounds of the reference sequence, provided there are reads that overlap in a contiguous series beyond the reference bounds.

  How many iterations did you try?

  Try setting iterations to to a higher number, say 1000 and see if that works.  Geneious will only perform as many iterations as required.

  If the assembly is to slow with a high iterative value, consider using menu Sequence -> Error correct and Normalize reads to Normalize (don't error correct) your reads.  This may substantially reduce the size of your data set and allow assembly to proceed faster with a high iterative setting.  Once you have generated an extended consensus you can map against that with the full read set to generate a final consensus.

  0

Please sign in to leave a comment.