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Old 10-11-2012, 12:12 AM   #1
Mithril
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Default Classify Bacterial and Archaeal fragments from 454-Metagenome

Hello all,
I have just started working with 454 metagenome datasets and was wondering if there is any tool that can classify reads from 454 into bacterial or archaeal sequences?

I have come across many tools that do something similar only for 16s rRNA.

Using a training dataset and word based classifier, can one divide the metagenome dataset into bacterial and archaeal sequences?

Thank you for your time!!
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Old 10-11-2012, 05:29 AM   #2
severin
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Default MGRast

Have you looked into MGRAST? It is a free webserver with lots of functionality.
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Old 10-11-2012, 06:21 AM   #3
Mithril
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Thank you for you suggestion.

Yes, I have. I would really like something that has a lot of standalone capacity instead of a webserver....
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Old 10-11-2012, 02:49 PM   #4
jimmybee
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MetaPhlAn (http://huttenhower.sph.harvard.edu/metaphlan/)
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Old 10-11-2012, 09:23 PM   #5
Mithril
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Thank you jimmybee! MetaPhlAn looks good.

Any more recommendations?

Once again, thank you for all your solutions.
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