Hi, everyone, I am trying Bowtie for reference based assembly. My draft genome dataset is not from a model organism, but a related species. This data contains ~20 million 88 bp illumina reads. Because it's not resequencing of reference genome, I need to use a relatively loose parameters. Actually I only focus on genes without caring about intergenic regions. A CDS dataset of model organism can be used as a reference in this assembly. What Bowtie parameters you suggest to use? Thank you very much.