My alignment rates with bowtie2 are ~95%, using paired-end reads on a de novo Trinity assembly. What I typically see in the literature is bowtie2 alignment rates of anywhere from 70-85% which is considered good.
What is the reason for the rates being so high? I know that it is because most of my reads are represented in the final set of contigs. I'm just trying to justify why my rates high compared to examples from the literature.
Any info would be great! Thanks.