bowtie2 code to bwa-mem2

Hi there,

I have this code, I would like to use the same options but would like to run bwa-mem2 instead.

bowtie2 -k 2 --very-sensitive –x GRCh38 -f input.fa | samtools view -bS -> output.bam

Is this the equivalent code?

bwa-mem2 -a GRCh38 input.fa | samtools view -bS -> output.bam

I am unable to convert the --very-sensitive

bwa-mem2 bowtie2

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written 3.6 years ago by Jalil Sharif •

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