Winnowmap
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Much more unmapped reads compared to minimap2
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.