MSA on bowtie2

[LilianK]

Hi guys,
I have two genome reads (one of them is in FASTQ format and the other one is in FASTA format) and I want to align them and call variants. I also have an already assembled reference genome.
Is it possible to run bowtie2 with two sets of read files and align them to one reference? (I tried and haven't succeed)
or- is it possible to index a read file and than align another read file to it?
I know that I might assemble one of those read files, but I wonder if I can avoid that.

many thanks!
Lilian.

[dpryan]

Just run bowtie2 twice, once for each set of reads. You can call SNPs on multiple samples, though I'm not sure how well that works with fasta reads (I've never tried).