Question: Is there a hybrid aligner that uses both long and short reads to align to a reference genome?
1
gravatar for NPL
23 days ago by
NPL10
NPL10 wrote:

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.

sequence alignment • 251 views
ADD COMMENTlink modified 21 days ago by d-cameron2.2k • written 23 days ago by NPL10

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

ADD REPLYlink written 23 days ago by JC11k
1

@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.

ADD REPLYlink modified 23 days ago • written 23 days ago by genomax89k

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

ADD REPLYlink written 23 days ago by JC11k

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.

ADD REPLYlink written 22 days ago by NPL10

Thanks. I will take a look at minimap2.

ADD REPLYlink written 22 days ago by NPL10
2
gravatar for d-cameron
21 days ago by
d-cameron2.2k
Australia
d-cameron2.2k wrote:

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).

ADD COMMENTlink modified 21 days ago • written 21 days ago by d-cameron2.2k

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

ADD REPLYlink written 20 days ago by NPL10

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

ADD REPLYlink written 20 days ago by genomax89k

Thank you for the response.

ADD REPLYlink written 20 days ago by NPL10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1733 users visited in the last hour