Entering edit mode
8.4 years ago
Apprentice
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170
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?
You probably don't have enough coverage to assemble a human genome but that said look at Canu.
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.
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.
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.
Thank you for comments. based on your advices, I try to do them!
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