Dear all,

I have indexed the C. elegans reference genome with:

bwa index output/genome/ref/seq/celegans.fa

and then aligned my de novo assembly to the reference with:

bwa mem -t 8 -x intractg output/genome/ref/seq/celegans.fa input/assembly/celegans/hgap/bristol/assembly.fa > output/alignment/pacbio/bwa/ref/bristolAssembly.sam

I then

samtools view -bS output/alignment/pacbio/bwa/ref/bristolAssembly.sam > output/alignment/pacbio/bwa/ref/bristolAssembly.bam

samtools sort output/alignment/pacbio/bwa/ref/bristolAssembly.bam -o output/alignment/pacbio/bwa/ref/bristolAssemblySorted.bam

samtools index output/alignment/pacbio/bwa/ref/bristolAssemblySorted.bam

to visualise the alignment in IGV.