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Old 07-03-2015, 03:41 AM   #1
dan.jo.di
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Location: Lisbon

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Default Bionumerics or CLC genomics Workbench?

Hello everyone!

I am starting with the analyses of some 5Mb bacterial genomes that were sequenced on illumina hiseq. I don’t need to do something very elaborate but I would like to quality filter, trim, assemble, annotate, check the main interest genes and compare it with some references sequences. For this type of non-programming analysis I heard that CLC genomics workbench and Bionumerics will be the best options. For both, I have the hypothesis of getting some specialized training. I tried both and it seems that CLC genomics is more user-friendly. What do think and what are the main advantages from each of them?

Thanks a lot.

dan.jo.di
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Old 07-03-2015, 03:48 AM   #2
GenoMax
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If you are primarily a biologist not familiar with using unix command line then one of the GUI-based programs is an easy option. If you are willing to learn/spend time on command line then multiple options will become available.

If you already have licenses available for the two programs you mention then go with the one you like. If you are still checking commercial programs out then look at Geneious.
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Old 07-07-2015, 05:27 AM   #3
dan.jo.di
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In fact, i'm not familiar at all with unix command and I do not have any skills to do so.
I don't have any licenses at the moment, I was asking precisely to make an informed decision when I buy one. Do you think Geneious is the best option? Can you tell me why do you think so? For sure it is cheaper than CLC or Bionumerics.

Thanks
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Old 07-07-2015, 05:57 AM   #4
GenoMax
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Most of these commercial packages have overlapping feature sets. Since all offer some sort of trial license you should make a decision about which one suits your needs best yourself.

You could also try and find a local collaborator to help you with the analysis. This could be a good project for a bioinformatics student to work on.
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