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 weeks 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 • 248 views
ADD COMMENTlink modified 11 weeks ago by WouterDeCoster22k • written 11 weeks 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 11 weeks ago by Brian Bushnell14k

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

ADD REPLYlink written 11 weeks 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 10 weeks 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 10 weeks ago • written 10 weeks ago by Brian Bushnell14k

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

ADD REPLYlink written 9 weeks ago by saranpons350
0
gravatar for WouterDeCoster
11 weeks ago by
Belgium
WouterDeCoster22k wrote:

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

ADD COMMENTlink written 11 weeks ago by WouterDeCoster22k

Thanks. Your link was helpful.

ADD REPLYlink written 10 weeks ago by saranpons350
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