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  • buthercup_ch
    Member
    • Apr 2014
    • 41
    #1

    Comparative genomics_35 bacterial strains

    Hi everyone,

    I'm currently dealing with the comparative analysis of the genome sequence of 35 bacterial strains.
    I AM NOT BIOINFORMATICIAN, but a former collaborator in a former project dealing with 7 strains used CD-HIT for clustering the common orthologs, and I was wondering if the same tool could be used to cluster 35 genomes.

    Is there any CD-HIT expert that could help me with this issue? If CD-HIT is not the tool…, any other suggestion?
    Tags: None
    • bioBob
      Member
      • Mar 2011
      • 72
      #2
      Hi, it might help to add some detail here. What is the source of your data? NGS? What did you currently have, SNP and INDEL lists or it sounds like you have predicted gene sequences??

        Comment

        • buthercup_ch
          Member
          • Apr 2014
          • 41
          #3
          Hi bioBob, thanks for you interest.
          The only material I have is a set of 35 genomes in .gb format. Obviously the original data were obtained by HTS in Illumina… ?? I don't know any other details. Some one perform the assembly and annotation and I received the .gb files.
          I'm afraid I can't help more than this.
          Last edited by buthercup_ch; 09-05-2014, 05:37 AM.

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