How to map reads shorter than 32bp with minimap2? I mapped fasta sequences to a reference. The fasta sequences range in length from 17bp up to several hundred bp. I used minimap2 with the following command: minimap2 -ax sr ref.fa seqs.fa, et cetera. Only the sequences greater than 32bp len mapped though.

samtools view -F 4 filename.sorted.bam | \
  cut -f10 | awk '{print length($1)}' | \
  sort | uniq -c | sort -k2 -n

   2304 32
  34931 33
   5443 34
   5343 35
   8811 36
   5485 37
   5417 38


Is it possible to make minimap2 map sequences shorter than 32bp? Do I need to use bwa aln or some other mapper?
Minimap2 doesn't work well with 32bp reads by design. Older mappers like bowtie1 and bwa-aln will be better.