aligning reads against shorter region

Question

[Juke34]

I would like to align 150bp reads against a reference region slightly shorter e.g 120bp from amplicon data. Would the alignment perform well or should we necessarily use a longer reference?

Answer 1

[pbpanigrahi]

Manual says

"Bowtie 2 is geared toward aligning relatively short sequencing reads to long genomes. That said, it handles arbitrarily small reference sequences (e.g. amplicons) and very long reads (i.e. upwards of 10s or 100s of kilobases), though it is slower in those settings. It is optimized for the read lengths and error modes yielded by typical Illumina sequencers."

You can explore --local option

[Juke34]

Thanks sounds the way to go with the --local.