I have a series of assemblies in fasta format from SOAP2 using different k values. I would like to merge the resulting assemblies to one file because some k values assemble parts that others don't, to create hopefully larger contigs. I thought I might be able to use oases to merge the files as this is what happens for the velvet/oases transcriptome assembly but not sure how I could do that. The commands don't appear to lend themselves to this application. Any ideas would be welcomed. I also have another three re-sequencing assemblies of different k values which could also try merging to this one re-sequencing data set.
A reference exists although as ~30 contigs, some are very large so it's quite good (there should be only four chromosomes in the genome).
I don't want to manually try to do this, I have already manually plugged some large N gaps in the first reference contig but too time costly and have not looked to stick contigs together yet either.