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

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!

bam bowtie2
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updated by Ram Ram • written by andrea.aguado.marin • andrea.aguado.marin

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.

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written by GenoMax GenoMax

1 answer

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.

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written by ATpoint ATpoint

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