Is there a hybrid aligner that uses both long and short reads to align to a reference genome?

Question

[NPL]

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.

[JC]

SPAdes or MIRA? you can pass short and long reads plus a reference sequence

[GenoMax]

@JC I guess you are referring to reference based assembly but OP is asking about mapping.

MIRA page says:

Do not use MIRA if you have PacBio or Oxford Nanopore reads.

Technically minimap2 could be used for both reads but not at the same time.

uses both short and long reads to improve the accuracy

Not sure how that will improve mapping accuracy. Reads are aligned one at a time.

[JC]

I am confused about what are the requirements then. OP, please clarify

[NPL]

Sorry for not being clear. @genomax is right. I am looking for a program that accepts and uses both short and long reads to improve mapping accuracy.

[NPL]

Thanks. I will take a look at minimap2.

Answer 1

[d-cameron]

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).

[NPL]

Thanks a lot for the answer. Which software do you recommend for correcting long reads using short ones?

[GenoMax]

Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone

[NPL]

Thank you for the response.