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Old 10-17-2013, 01:22 AM   #1
tigerxu
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Default Best approach to analyze taxonomic profiling of metagenomes from environmental sample

I'm wondering which tool currently available is best for analyzing taxonomic profiling of environmental microbial community (non-human microbiome), e.g. soil, marine, sediment? I suppose that the analysis need to be done with all reads but not contigs.

Thanks in advance!
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Old 10-17-2013, 03:26 AM   #2
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I think mg-rast is a pretty great way to start..
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Old 10-17-2013, 03:53 AM   #3
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Thank you rhinoceros!

I forgot a point. I hope to find a standalone software not web-based server. As MG-RAST or IMG is sometimes long waiting. I'm wondering if there is other fast and local approach. I knew MEGAN but searching NCBI NR is time-consuming.
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Old 10-17-2013, 03:58 AM   #4
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Quote:
Originally Posted by tigerxu View Post
Thank you rhinoceros!

I forgot a point. I hope to find a standalone software not web-based server. As MG-RAST or IMG is sometimes long waiting. I'm wondering if there is other fast and local approach. I knew MEGAN but searching NCBI NR is time-consuming.
I don't know about IMG but I've sent dozens of samples to mg-rast and always gotten results within a few days. As to the speed of local approach, it depends on what kind of hardware you have, and of course, what you're doing. With a few hundred core server things can be done fast, not so with your average desktop. But consider e.g. the difference between working with raw reads and binned reads..
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Last edited by rhinoceros; 10-17-2013 at 04:01 AM.
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Old 10-17-2013, 04:03 AM   #5
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Sure, I will try MG-RAST. Thanks!
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