Question: De novo assembly
0
gravatar for Huynh Nguyen
3.1 years ago by
Huynh Nguyen0 wrote:

Dear all,

Please let me know if I could use CLC Genomic Workbench 8.0 for De novo metagenomic assembly.

Thanks you all so much.

sequencing next-gen assembly • 939 views
ADD COMMENTlink written 3.1 years ago by Huynh Nguyen0

Ask CLC, it's a commercial product, they'll answer your phone call.

ADD REPLYlink written 3.1 years ago by Devon Ryan90k

I will try, thank you so much.

ADD REPLYlink written 3.1 years ago by Huynh Nguyen0

You will need a license for the microbial genomics module for CLC which requires a separate license. Check with CLC support.

ADD REPLYlink written 3.1 years ago by genomax68k

If you're looking for an alternative, a common assembler is Canu. Not sure what type of reads you have though.

ADD REPLYlink written 3.1 years ago by WouterDeCoster39k

Some information about my project: We aim to investigate diversity of microbial community in forest soil. In addition, we also focus on mining genes encoding laccase enzyme.

  • DNA: isolated from forest soil
  • Sequencer: Illumina Hiseq 2500

I sent my DNA samples to Baseclear company (in Netherlands). After that they gave me paired-end raw sequences and assembled sequence that was assembled using CLC Genomic Workench 8.0. I don't know that this Workbench was optimized for metagenomic de novo assembly. Is this method good enough for downstream bioinformatics analysis?

Thank you all for your help!

ADD REPLYlink modified 3.1 years ago • written 3.1 years ago by Huynh Nguyen0

I am not sure you can use canu in this case.
You may want to try SPAdes or metavelvet. Both will require knowledge of unix/command line along with access to a proper server with enough RAM etc.

ADD REPLYlink written 3.1 years ago by genomax68k

Right, illumina sequencing. You're right and Canu is not appropriate here. Just back from London Calling (Oxford Nanopore Conference) :-)

ADD REPLYlink written 3.1 years ago by WouterDeCoster39k

Thanks but what do you think about CLC Genomic workbench? Is it appropriate? I have already received assembled results from Baseclear and I am confusing about this results.

ADD REPLYlink written 3.1 years ago by Huynh Nguyen0

I don't know if there is a difference between the CLC genome assembler (and the one provided by CLC microbial genomics module). You are going to have to contact Baseclear and ask them which one they used for the assembly. Then call/email CLC tech support and ask them about difference, in case Baseclear did not use the microbial one. If they say that there are no differences then you should be able to go ahead with whatever else you want to do with this assembly.

If you want to start from scratch with fastq reads, we have given you a couple of options above.

ADD REPLYlink modified 3.1 years ago • written 3.1 years ago by genomax68k

Thanks so much for your suggestions.

ADD REPLYlink written 3.1 years ago by Huynh Nguyen0
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