I am trying to assemble a low coverage 454 data of a plant using Newbler. I have two raw sff files from two different genotypes of my experimental plant. newbler completes the assembly step without a considerable error for the individual sffs. But when I try to assemble the sff files of both genotypes together(using incremental denovo assembly) it just adds up the total contigs and the singletons for that matter neglecting the possible common contigs between the two genotypes. To my understanding newbler is treating every read in both the sff files as unique which is very unlikely to happen. My basic aim is to find the SNPs and repeats in the genome and if newbler is assembling every read into a unique contig then this could be a matter of concern to me. Please provide the necessary explaination for this behaviour.
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