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Question: tools for amplicon analysis
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gravatar for Lena.Rueschstroer
4.4 years ago by
Lena.Rueschstroer • 0
Germany
Lena.Rueschstroer • 0 wrote:

Dear all,

I was wondering if somebodys knows if there are specific tools for checking the alignment of amplicons, optimizing it and account for slight mismatches?  I am trying to establish an internal best practice guide for amplicon analysis and I am following this guide:

http://qcbs.ca/wiki/guide_to_amplicon_sequencing_experiment.

Now I can't find the tools for the steps named above. For the step: "remove chimeras" I found the Uchime tool.

 

Thanks,

Lena
amplicon tool alignment • 1.2k views
ADD COMMENT • link •
modified 4.4 years ago by Bjoern Gruening ♦ 5.1k • written 4.4 years ago by Lena.Rueschstroer • 0
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gravatar for Bjoern Gruening
4.4 years ago by
Bjoern Gruening ♦ 5.1k
Germany
Bjoern Gruening ♦ 5.1k wrote:

Hi Lena,

have you looked at the Galaxy Tool Shed? CD-Hit for example should be there: http://toolshed.g2.bx.psu.edu/view/jjohnson/cdhit

Cheers,

Bjoern
ADD COMMENT • link written 4.4 years ago by Bjoern Gruening ♦ 5.1k
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