Two references 1. genome 2. plasmid for bowtie2

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

This is the methodology used

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 ?

wgs bacterialgenomics alignment

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updated 2.4 years ago by GenoMax 16K • | written 2.4 years ago by RT 0

1 answer

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

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written 2.4 years ago by GenoMax 16K

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