I guess I decided to ask all the questions of this week today. I have a model organism which has not yet been sequenced. So I would go for denovo assembly. I will be running the data on multiple lanes as replicates for the same sample.
How will this affect my Genome assembly?
Are there chances of getting erroneous contigs?
Will most of my reads be discarded as k-mer filter might think of the other replicates as repetitive or false positive k-mers and discard them?
Is there any specific assembler which might avoid the above problems?
Or will it just affect the computational resources?