Two references 1. genome 2. plasmid for bowtie2

Question

[RT]

Hello, I am working on aligning my raw reads onto reference genome and plasmid

In this paper, they used SMALT tool but I am using Bowtie2 in my WSL. How do I align my reads on both the references on bowtie2 ?

Answer 1

[GenoMax]

You can simply cat all reference sequences together. Create an index file with bowtie2 and then align as usual.