PACBIO contigs with BWA-MEM

[khush876]

Hi,

I have assembled a plant genome using PACBIO and would like to add ILLUMINA data for finishing up. However, I am not sure how to proceed with it.

bwa mem pacbio.ref.fa reads1.fastq reads2.fastq > aln.sam

or

bwa mem -x pacbio.ref.fa reads1.fastq reads2.fastq > aln.sam

Any suggestion?

[lh3]

bwa index ref.fa
bwa mem -t16 ref.fa read1.fq read2.fq

[khush876]

thanks