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7.5 years ago
chongchu.cs
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Are there any tools specifically designed to align short reads to Pacbio or nanopore long reads?
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Why do you need a separate tool? Once you convert your long reads into fasta/multi-fasta all NGS aligners will work. At that point those reads are just a reference to align to.
You mean using tool like bwa or blasr? I just worry about the high error rates.
The way you phrased your question it says that you want to align a set of short reads to a set of long reads (actually just the sequence from those reads). At that point the long reads are acting as a reference (without the question of error rates coming into play).
If you are interested in correcting your long reads using the short sequences then you may want to follow this tutorial.
PacBio and Nanopore technologies are evolving at a fast pace. Your data is from early or recent iterations? For example, I think recent PacBio has very low error rate and you could use BWA to align short reads onto these long reads.
Anyway, what you want to do? If you want to correct long, noisy reads with Illumina reads, just search for "correction" instead of "alignment", there are several tools designed for that.
The error rates for latest long reads is very low? How low they are? This is a question asked from a cooperate biologist, they have low coverage Pacbio long reads and short reads, want to use the long reads to link some fragmented repeat contigs.
Get the PacBio version of their reads and look at the error rate on PacBio site.
Where do the short reads enter here? Anyway, it seems you need to google for "hybrid assembly" or "long reads scaffold".
Hint: look at Allpaths-LG, probably SPAdes can deal with this combination as well.
I know they say the error is now lower. But I just saw pacbio results 2 days ago...and there really was alot of errors. Now whether previous versions was used I dont know.....but I certainly will be recommending the corrections mapping
that would be no senseļ¼cause the reference is error-prone.