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  • Using CLARK and EBI for metagenomes

    Hello there,

    Given Lindgreen et al. 2016 (http://www.nature.com/articles/srep19233), 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.

  • #2
    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:
    TaxaName,Lineage,Count,Proportion_All(%),Proportion_Classified(%)
    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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    • #3
      Dear all,

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

      Name,TaxID,Lineage,Count,Proportion_All(%),Proportion_Classified(%)
      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:


      Best,
      Rachid
      Last edited by rouni001; 04-14-2016, 12:46 PM.

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