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Old 04-07-2016, 04:00 AM   #1
Junior Member
Location: Aberystwyth

Join Date: Sep 2015
Posts: 2
Lightbulb Using CLARK and EBI for metagenomes

Hello there,

Given Lindgreen et al. 2016 (, I am thinking of trying and use CLARK as a pre-processing/taxonomical analysis tool and the EBI webserver for functional analysis.

I am worried, however, that going from processing the raw files and analysis taxonomy with CLARK to functional analysis with EBI may cause problems.

Does CLARK output EBI-friendly files?

Anyone with background to give some input on this?

Thanks in advance.
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Old 04-07-2016, 07:48 AM   #2
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Location: California

Join Date: Jul 2014
Posts: 198

Are you talking about the EBI Metagenomics service? Seems like they want to start with raw fastq files (after human contaminant removal if applicable).

You might have to contact them about providing intermediate input. FWIW, here are a few lines of what the CLARK output looks like:
Acanthamoeba polyphaga mimivirus,;;;;Mimiviridae;Mimivirus,1,9.8806e-05,0.000131404
Acanthocystis turfacea Chlorella virus 1,;;;;Phycodnaviridae;Chlorovirus,1,9.8806e-05,0.000131404
Acetobacter pasteurianus,Bacteria;Proteobacteria;Alphaproteobacteria;Rhodospirillales;Acetobacteraceae;Acetobacter,4,0.000395224,0.000525615
Acetobacterium woodii,Bacteria;Firmicutes;Clostridia;Clostridiales;Eubacteriaceae;Acetobacterium,2,0.000197612,0.000262807
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Old 04-14-2016, 12:33 PM   #3
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Location: LA

Join Date: Apr 2016
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Dear all,

In the latest version (v1.2.3), the output (abundance) produced by CLARK rather looks like:

Acanthamoeba polyphaga mimivirus,212035,;;;;Mimiviridae;Mimivirus,1,3.24058e-05,5.77055e-05
Acanthocystis turfacea Chlorella virus 1,322019,;;;;Phycodnaviridae;Chlorovirus,1,3.24058e-05,5.77055e-05
Acaryochloris marina,155978,Bacteria;Cyanobacteria;;Chroococcales;;Acaryochloris,9,0.000291652,0.00051935
Acetobacter pasteurianus,438,Bacteria;Proteobacteria;Alphaproteobacteria;Rhodospirillales;Acetobacteraceae;Acetobacter,8,0.000259246,0.000461644
Acetobacterium woodii,33952,Bacteria;Firmicutes;Clostridia;Clostridiales;Eubacteriaceae;Acetobacterium,22,0.000712927,0.00126952

The reported NCBI taxonomy id is what is needed to process organisms (with their read count) detected by CLARK.
If you have a specific need for your analysis then please feel free to post it in the forum of CLARK users:!forum/clarkusers


Last edited by rouni001; 04-14-2016 at 01:46 PM.
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clark, ebi, metagenomes

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