Question: Where i can find sequencing reads(3rd generation sequencing) data set in which each read length is above 1000bp?
1
gravatar for saranpons3
19 months ago by
saranpons360
saranpons360 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 • 938 views
ADD COMMENTlink modified 19 months ago by WouterDeCoster37k • written 19 months ago by saranpons360
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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 19 months ago by Brian Bushnell16k

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

ADD REPLYlink written 19 months ago by saranpons360

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 19 months ago by saranpons360
1

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 19 months ago • written 19 months ago by Brian Bushnell16k

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

ADD REPLYlink written 19 months ago by saranpons360
0
gravatar for WouterDeCoster
19 months ago by
Belgium
WouterDeCoster37k wrote:

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

ADD COMMENTlink written 19 months ago by WouterDeCoster37k

Thanks. Your link was helpful.

ADD REPLYlink written 19 months ago by saranpons360

Hi WouterDeCoster

Any links for nanopore whole exome public datasets?

ADD REPLYlink written 4 weeks ago by bioExplorer3.7k

Nanopore sequencing is not suitable for exome sequencing.

ADD REPLYlink written 4 weeks ago by WouterDeCoster37k

can you elaborate on that ?

ADD REPLYlink written 4 weeks ago by bioExplorer3.7k
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Whole exome sequencing does the following: shearing reads to short fragments, amplify with PCR, use target capture with oligonucleotides followed by another round of amplification. While all of these things work for nanopore sequencing it's really not optimal. Nanopore sequencing doesn't need PCR (preferentially no amplification used) and will generate 10kb and longer reads, which is by far longer than your average exon.

ADD REPLYlink written 4 weeks ago by WouterDeCoster37k

+1 Thanks WouterDeCoster

ADD REPLYlink written 4 weeks ago by bioExplorer3.7k
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