Question: Where i can find sequencing reads(3rd generation sequencing) data set in which each read length is above 1000bp?
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gravatar for saranpons3
4 months ago by
saranpons350
saranpons350 wrote:

Dear Members, I'm looking for downloading sequencing reads(3rd generation) whose length is above 1000bp. It would be helpful for me if anybody can provide me with proper links. Also, I would like to know that what should be the size of K when we assemble reads from 3rd generation sequencing technologies. I guess that K value should be large. Is my guess correct?

reads • 304 views
ADD COMMENTlink modified 4 months ago by WouterDeCoster24k • written 4 months ago by saranpons350

You don't normally use kmer-based (or purely kmer-based) assembly for single-molecule sequencing reads; the error rate is too high. Instead, you use all-to-all alignment and consensus.

ADD REPLYlink written 4 months ago by Brian Bushnell15k

Dear Brian, Is all-to-all alignment and consensus mean Overlap-Layout-Consensus(OLC) approach?

ADD REPLYlink written 4 months ago by saranpons350

Dear Brian, I have read Kmer has many applications in many bioinformatics analysis (https://en.wikipedia.org/wiki/K-mer). So, I'm not concerned the length of Kmer only for assembly problem. Generally, for other bioinformatics applications, what would be the length of K-mers for the lengthier reads generated by 3rd generation sequencing machines such as nanopore and pacbio. Can we go for the kmer length above 520?

ADD REPLYlink written 4 months ago by saranpons350

As I said, kmers are unsuitable for long single-molecule read assembly. Other approaches like OLC or string graphs are used. You're certainly welcome to try k=520 with long reads, and see what happens. But typically people use string-based assemblers like Falcon or Celera.

ADD REPLYlink modified 4 months ago • written 4 months ago by Brian Bushnell15k

Thanks for your answer. I'll get back to you if I have other questions related to this.

ADD REPLYlink written 4 months ago by saranpons350
0
gravatar for WouterDeCoster
4 months ago by
Belgium
WouterDeCoster24k wrote:

A ton of Oxford Nanopore data from NA12878 is available here.

ADD COMMENTlink written 4 months ago by WouterDeCoster24k

Thanks. Your link was helpful.

ADD REPLYlink written 4 months ago by saranpons350
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