Multiple segments of reference virus

Question

[lxu2011ct]

Hi, I'm new to Bowtie2 and want to generate the indexer with Bowtie2-Build from a multiple-segment reference virus. I downloaded it from NCBI as one fasta file with multiple sequences (segments) in the file. I want to know if Bowtie2-Build can run with one fasta file with multiple sequences. If not, I will break it into multiple fasta files with one sequence in each file, then feed them as comma-separated list of the fasta files. Thank you very much.

Answer 1

[GenoMax]

Yes it can and you should do it that way. File would have to be in multi-fasta format.

[lxu2011ct]

Thank you very much.