Question: Any tool designed to align short reads to long reads?
0
gravatar for chongchu.cs
3.4 years ago by
chongchu.cs10
United States
chongchu.cs10 wrote:

Are there any tools specifically designed to align short reads to Pacbio or nanopore long reads?

sequence next-gen alignment • 1.5k views
ADD COMMENTlink modified 8 months ago by Biostar ♦♦ 20 • written 3.4 years ago by chongchu.cs10
1

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.

ADD REPLYlink written 3.4 years ago by genomax90k

You mean using tool like bwa or blasr? I just worry about the high error rates.

ADD REPLYlink written 3.4 years ago by chongchu.cs10
1

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.

ADD REPLYlink written 3.4 years ago by genomax90k
1

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.

ADD REPLYlink written 3.4 years ago by h.mon31k

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.

ADD REPLYlink written 3.4 years ago by chongchu.cs10

How low they are?

Get the PacBio version of their reads and look at the error rate on PacBio site.

they have low coverage Pacbio long reads and short reads, want to use the long reads to link some fragmented repeat contigs.

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.

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by h.mon31k

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

ADD REPLYlink written 3.4 years ago by YaGalbi1.5k

that would be no senseļ¼Œcause the reference is error-prone.

ADD REPLYlink written 3.4 years ago by shenwei3565.3k
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