Getting the consensus file from a reference based alignment

[rpbaptista]

Hi,

I have a Mapped genome fasta file with chromosomes scaffolds and a denovo contigs sequences all together in a Multifasta file.
I aligned them to a multifasta reference genome (each sequence is a chromosome) using Nucmer (from Mummer), and some of my gaps were filled as I expected for the divergences , but I couldnt take the consensus fasta file from this Nucmer alignment, does someone have an idea about how could I make it? Or other genome aligner that works like Nucmer that gave me the same result?
(My genome is highly similar to this Reference)
thanks

[tw7649116]

Dear rpbaptista:
I have the same problem now. How can you solve the problem?
I used SOAPdenovo get the scafseq,how can I use the reference to get the consensus sequence?
Thank you！

[rpbaptista]

Hi tw7649116,

Try to use ABACAS. http://abacas.sourceforge.net/

hope it helps you

[Matt Kearse]

The free (unlicensed) version of Geneious can do what you want. It also has an option to fill the consensus with either the reference sequence bases or Ns when either the coverage or quality of the aligned sequences are below a specified threshold.

[tw7649116]

Thank you very much！I'll try!!

[tw7649116]

Hi tw7649116,

Try to use ABACAS. http://abacas.sourceforge.net/

hope it helps you

I have many sequences need to be aligned to get the consensus sequence.
Is there any command line software can do this?
Thank you!