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Old 03-29-2012, 02:36 AM   #1
fanyucai1
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Default SOlid &&&& Metagenomics

Are there some research to Metagenomics using Solid???? Otherwise, the short read (about 50bp)to apply thie field????
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Old 03-29-2012, 04:01 AM   #2
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Are you looking for software, or asking about whether people have used Solid in metagenomics so far ?

I think de novo assembly is a little trickier, but I'm not worried about the read length for our chosen analysis techniques.
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Old 03-29-2012, 05:42 AM   #3
fanyucai1
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Quote:
Originally Posted by colindaven View Post
Are you looking for software, or asking about whether people have used Solid in metagenomics so far ?

I think de novo assembly is a little trickier, but I'm not worried about the read length for our chosen analysis techniques.
Thank you for your reply. I want to know whether some papers about Metagenomics on the basic of Solid sequencing.
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Old 03-30-2012, 04:43 AM   #4
colindaven
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From the website
http://www.appliedbiosystems.com/abs...ns.html#anchor

Metagenomics

Metatranscriptomic analyses of chlorophototrophs of a hot-spring microbial mat
Publication: The ISME Journal (2011)
Authors: Liu Z. et al.

Confirmation of the Sequence of 'Candidatus Liberibacter asiaticus' and Assessment of Microbial Diversity in Huanglongbing-Infected Citrus Phloem Using a Metagenomic Approach
Publication: Molecular Plant-Microbe Interactions, Vol. 22, No. 12, 2009
Authors: Tyler et al.

The carnivorous bladderwort (Utricularia, Lentibulaiceae) a system inflates
Publication: Journal of Experimental Botany, vol. 61, No1, pp 5-9, 2010
Authors: Albert, et al.
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Old 03-30-2012, 04:45 AM   #5
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In the NCBI SRA there are a couple more studies too, which may not be published:


1.
SOLiD sequencing of HLB infected Citrus phloem
1 ABI_SOLID (AB SOLiD System) run: 337.1M spots, 11.8G bases, 12.2GB downloads
Accession: SRX004995

CEG 50-50nt mate-pair library for sample GG3
1 ABI_SOLID (AB SOLiD System 3.0) run: 315.6M spots, 31.5G bases, 26.1GB downloads
Accession: SRX105134

25.
ABI 50-50nt mate-pair library for sample GG2
1 ABI_SOLID (AB SOLiD System 3.0) run: 281.8M spots, 27G bases, 22.3GB downloads
Accession: SRX105133

26.
ABI 75nt fragment library for sample GG1
2 ABI_SOLID (AB SOLiD System 3.0) runs: 339.8M spots, 25.5G bases, 20.7GB downloads
Accession: SRX105132

27.
CEG 35nt fragment library for sample GG1
1 ABI_SOLID (AB SOLiD System 2.0) run: 171.6M spots, 6G bases, 5.2GB downloads
Accession: SRX105131
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Old 03-30-2012, 05:59 PM   #6
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Thank you for reply. I will try it.
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Old 04-03-2012, 03:52 AM   #7
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The last 4 datasets mentioned are very nice, and are from

Iverson et al 2012, Science.
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Old 01-21-2013, 09:08 PM   #8
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Thanks colindaven, neat papers, esp. genome-from-metagenome one. And yet I still have a question: is it even possible to use raw color-space reads (ie no assembly, no transforming to base space) to analyse a metagenome? As I've heard, BFAST and some other tools can do alignment of .csfasta against reference genome, but will they work against, say, NCBI database?

Last edited by A_Morozov; 01-21-2013 at 09:08 PM. Reason: Just fixing orthography
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