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
11 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?

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ADD COMMENTlink modified 11 months ago by WouterDeCoster30k • written 11 months ago by saranpons350
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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 11 months ago by Brian Bushnell15k

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

ADD REPLYlink written 11 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 11 months ago by saranpons350
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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 11 months ago • written 11 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 11 months ago by saranpons350
0
gravatar for WouterDeCoster
11 months ago by
Belgium
WouterDeCoster30k wrote:

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

ADD COMMENTlink written 11 months ago by WouterDeCoster30k

Thanks. Your link was helpful.

ADD REPLYlink written 11 months ago by saranpons350
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