Much more unmapped reads compared to minimap2

[yipukangda]

Hi,
A fq file is mapped with minimap2 and Winnowmap simultaneously for removing host reads, but Winnowmap is nearly 5 times more reads left than Winnowmap, here is the command:

minimap2 -ax map-ont -t 32 ref.fa seq.fq | samtools fastq -n -f 4 - > host_clean_minimap.fastq # 22,998 reads left
winnowmap -W repetitive_k15.txt -ax map-ont ref.fa seq.fq | samtools fastq -n -f 4 - > host_clean_winnow.fast # 103,014 reads left

Could winnowmap do better if changing some parameters?

Thanks.