minimap2 finds max. 51 occurences of marker sequence in about 500 genomes

[ms-gx]

I am searching a specific sequence in about 500 bact. genomes which should occur in all of them with very slight variations. That means the genomic region has a similarity of >99.5%.
Length of the region is about 500 bp.

My call is:
minimap2 -cx asm20 all_genomes.fasta marker_sequence.fasta > result1.minimap2

Version: 2.16-r922

Is there some specific parameter causing this?

[lh3]

Option -N, which is set to 50 with -x asm20.

[ms-gx]

Uhhh... that easy. Thanks a lot!
Although, if I am not mistaken, the manpage does not mention this. Maybe adding this to manpage would be helpful.

Thank you!

[lh3]

It is in the manpage, as well as the command-line help.

[ms-gx]

What I meant is the fact that -x asm20 sets N=50. Or is this really on the manpage and on the command-line help?

[tseemann]

@ms-gx I agree with you, I have filed a separate issue.