Question: Software For Hiseq/Pacbio Hybrid Assembly In Human Genome
0
gravatar for Apprentice
2.8 years ago by
Apprentice20
Apprentice20 wrote:

Hi,

I would like to known whether there is a free software that can effectively combine IlluminHiseq and PacBio reads in a human genome assembly.

The Hiseq is Hiseq2500, The whole genome sequencing is obtaining ∼30x sequencing coverage. The PacBio's chemistry is P6-C4. The whole genome sequencing is obtaining ∼15x sequencing coverage.

Could you give me any advice?

pacbio assembly • 1.1k views
ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by Apprentice20
1

You probably don't have enough coverage to assemble a human genome but that said look at Canu.

ADD REPLYlink written 2.8 years ago by genomax65k

Hi Canu!

Thank you for your comment. Could you give me the source for your opinion ?

I've read the website about genome assembly with PacBio long reads. https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/Large-Genome-Assembly-with-PacBio-Long-Reads

According to the website, if I do the de novo assembly, the coverage is not enough. But, if I do the hybrid assembly, it seems that our coverage (∼15x) is enough.

ADD REPLYlink written 2.8 years ago by Apprentice20
1

You can try the different options mentioned in this thread. Lot of times these assemblies are dependent on quality of libraries. If your libraries happen to have the right long fragments the results could be very good but if not then YMMV.

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by genomax65k
1

You can try the DBG2OLC assembler, it works for hybrid assembly with not so high coverage.

Just curious - why would you try to denovo assemble a human genome, any assembly you do with your data would not be comparable to the available genome.

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by Rohit1.3k

Thank you for comments. based on your advices, I try to do them!

ADD REPLYlink written 2.8 years ago by Apprentice20

as suggested previously with the coverage you have you can use Canu or DBG2OLC

But there is still a lot of tools that you need to discover maybe it suits what you want https://en.wikipedia.org/wiki/Sequence_assembly
https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/Large-Genome-Assembly-with-PacBio-Long-Reads

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by Medhat8.2k
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