Question

assembly of large Genome(tool)

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8.8 years ago

midox ▴ 290

hello,
I wanted to know what is the most appropriate tool assembler for data from a large "large genome" as the plant genome? according to your experiences.
thank you

Assembly large génome NGS • 1.7k views

ADD COMMENT • link updated 16 months ago by Ram 43k • written 8.8 years ago by midox ▴ 290

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What kind of library do you have? Do you have PacBio reads or not? Based on what you have there will be different stratify

ADD REPLY • link updated 16 months ago by Ram 43k • written 8.8 years ago by Medhat 9.7k

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yes I have PacBio Reads .
and I want to find an assembler which is adaptable to wide assembled Genome

ADD REPLY • link 8.8 years ago by midox ▴ 290

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you have PacBio with illumina to correct or only PacBio

ADD REPLY • link 8.8 years ago by Medhat 9.7k

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yes, i have PACBIO with Illumina.

ADD REPLY • link 8.8 years ago by midox ▴ 290

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https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/Large-Genome-Assembly-with-PacBio-Long-Reads

ADD REPLY • link 8.8 years ago by Medhat 9.7k

score 2 · Answer 1 · 2015-06-21

The best assembler I've been exposed to is the the one developed by NRGene on maize. They specialize in the complex plant genomes while most other assemblers were developed to be used on human or animal systems. Here's one of the press releases on their work in maize:

http://www.bigdatanews.com/group/bdn-daily-press-releases/forum/topics/big-data-genomic-analysis-delivers-complete-corn-genome-in-34-hou

Good luck to you!