I have both short (illumina) and (pacbio) long reads of the same sample and I want to align it to a reference genome. I know there are many aligners, but I was wondering if there is one that uses a hybrid method, i.e. uses both short and long reads to improve the accuracy. I know that unicycler, for example, does a hybrid de novo assembly. However, I am looking for a program that does hybrid alignment to a reference genome. My google search did not find anything. Any comment would be appreciated.
No such hybrid aligner exists since aligners perform read alignment independently for each fragment. That is: per read for long read, and per read pair for paired-end short read sequencing. A 'hybrid' approach would give the same results as aligning the short and long reads independently with the same aligner.
Short and long reads can be combined by 'hybrid' methods either prior to alignment (using short reads to correct long reads, or perform de novo assembly), or after alignment (reference-guided assembly/alignment adjustment/variant calling based on the aligned short+long reads).