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  • How to do genome statistics from fasta and .gz file

    Hello everyone,

    I'm new in this field. Now i have 3 types of files downloaded from public database :
    (1) contigs sequence in .gz format
    (2) scaffolds sequence in .fasta format
    (3) transcriptomes sequence in .fasta format

    I don't know what are the steps i should do to get the statistics data (number of scaffolds, N50 count scaffolds, number of contigs, min length of contig, etc). I know i have to run it on linux and maybe using some perl script?

  • #2
    Hani,

    You can download BBTools and run the included "stats.sh" script. In Linux, the command would be:

    stats.sh in=contigs.fasta

    But you don't HAVE to run it on Linux, you just need Java installed. In Windows, for example, if you unzip the bbtools package to "C:\bbmap\", the command would be:

    java -Xmx200m -cp C:\bbmap\current\ jgi.AssemblyStats2 in=contigs.fasta

    The tool works on fasta files whether or not they are gzipped.

    Comment


    • #3
      Hello Brian,

      Thank you for the reply. Is BBTools same with BBMap?
      Where should i put my .fasta file? in /current/ folder?

      Comment


      • #4
        Yes, BBMap and BBTools are the same package.

        You can put the fasta files anywhere, it doesn't matter, as long as you specify a path. For example, if you put a fasta files in /usr/stuff/contigs.fasta, and bbmap is at /usr/programs/bbmap/, then the command would be:

        /usr/programs/bbmap/stats.sh in=/usr/stuff/contigs.fasta

        Comment


        • #5
          Hello again,

          Why when i'm using stats.sh in=contigs.fasta in Linux, i get :
          -bash: stats.sh: command not found ?

          Comment


          • #6
            The shell script just isn't in your $PATH.

            Comment


            • #7
              The simplest way to resolve this is to type "./stats.sh", if you are in the same directory, or use the full absolute path otherwise.

              Comment

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