it is possible to use bowtie2 to align fasta files rather than fastq? essentially I would like to use bowtie just like an aligner such as muscle, taking advantage of the greater computational speed of the former. In the handbooks I found that this is possible but there is no example.
I created a reference sequence ref_idx with bowties2-build; if input.fa is the file i want to align, what would be the syntax? I wrote:
bowtie2 -q -x ref_idx -U input.fa -S output_aln
but I got the error: Error: reads file does not look like a FASTQ file terminate called after throwing an instance of 'int' Aborted (core dumped) (ERR): bowtie2-align exited with value 134
If this is possible, would bowtie work also with multifasta files?