Cfrgtkky

PacBio provides longer read length than Illumina's short-length reads. Longer reads offer better opportunity for genome assembly, structural variant calling. It is not worse than short reads for calling SNP/indels, quantifying transcripts. Sounds like PacBio can do whatever Illumina platform can offer.

Would that be any reason for going with Illumina if PacBio's long reads can do everything and more?

There are so many reasons why one might want to prefer Illumina over PacBio (also note that it's a false dichotomy, at least Oxford Nanopore is a competitive sequencing platform):

• The first (IMHO and the most common reason) is still the cost of both sequencing and the instruments. Illumina can sequence a Gbp of data for $7 - $93. PacBio sequencing is according the same webpage $115 per Gbp, however at our sequencing center it's ~$200. Though ONT might have already a cheaper solution. Edit, I just found a google sheat with prices that seems to be frequently updated, seems that the ratio still holds Illumina short reads ~10x cheaper than PacBio.


• RNA-seq (i.e. analysis of a gene expression) is not possible with PacBio due to preferential sequencing of smaller fragments; shorter genes would always be shown to be more expressed. To be clear, it's possible to sequence RNA with PacBio (the keyword is iso-seq), but the analysis of gene expression is problematic.


• It's way easier to extract fragmented DNA (concerns small non-model organisms; although recently a single mosquito was sequenced, so we can expect a further improvement)


• other sequencing techniques as RAD-seq that allow genotyping with very little effort and cost, I have never seen anybody even considering using long reads for such genotyping


• 
  Genome profiling (assembly-less genome evaluation) based on kmer spectra analysis is not possible with PacBio data due to higher error rates. Conflict of interest: I am a developer of one of the tools for genome profiling (smudgeplot)


• I bet there will be a plenty other applications I am not aware of

Three reasons for Illumina:

* Much better for a large number of samples (easily handle 96 samples). 

* SNP calling is much better - much greater depth

* Hardware costs, an Illumina MiSeq machine is cheap 

PacBio SNP calling has been improved towards the standard of Illumina by DNA modification to the inputs to be sequenced but it depends on the application.

Many analyses performed on Illumina machines these days require large numbers of reads. For example, most analyses in ChIP-seq, RNA-seq, ATAC-seq etc, need 10s or even 100s of millions of reads for the statistics to work out properly.

But this isn't limited to just sequencing as an assay experiments. High depths are important for things like somatic variant calling as well. Or simply sequencing of medical gene pannels, where you might only have 20 amplicons of a 500bp each, but need to do it on 100s of patients as cheaply as possible.