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
15 days ago by
saranpons340
saranpons340 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 • 182 views
ADD COMMENTlink modified 15 days ago by WouterDeCoster20k • written 15 days ago by saranpons340

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 15 days ago by Brian Bushnell13k

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

ADD REPLYlink written 15 days ago by saranpons340

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 8 days ago by saranpons340

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 8 days ago • written 8 days ago by Brian Bushnell13k

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

ADD REPLYlink written 7 days ago by saranpons340
0
gravatar for WouterDeCoster
15 days ago by
Belgium
WouterDeCoster20k wrote:

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

ADD COMMENTlink written 15 days ago by WouterDeCoster20k

Thanks. Your link was helpful.

ADD REPLYlink written 14 days ago by saranpons340
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