Could bowtie2 use a fasta file as input to be mapped against a reference genome?

Question

[andrea.aguado.marin]

Hello! My name is Andrea and currently I am working with SARS-CoV-2 sequences, in order to identify different quasispecies within given samples. Thereby, I would like to know if I could map the fasta files that I obtain as ouput of my process (corresponding every fasta to a different low-frequency variant identified in the same sample) to the SARS-CoV-2 canonical reference genome.

Thanks in advance!

[GenoMax]

If your fasta sequences are long then consider using a different aligner that can look for local alignments or be sure to add --local flag to bowtie2.

Answer 1

[ATpoint]

Yes, bowtie2 can align fasta files, see the manual: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml

It is the -f flag you have to set.