# 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 is not the most optimal aligner in this case, it was designed for long reads, of which 32bp reads are clearly not. You could try lowering the mnimizer k-mer length and with -k the default being 15, also try lowering the minimzer window size with -w. However I suggest using bwa aln and bwa samse for all reads under 32bp and then merging the alignment later. Although I struggle to see what the utility of these short reads will be against a backdrop of longer reads?

• They aren't really reads per se - just short sequences from another application that I need to align. Thanks for your comments. Aug 21 '18 at 21:32

Minimap2 doesn't work well with 32bp reads by design. Older mappers like bowtie1 and bwa-aln will be better.