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  • GC content of assembled transcripts

    Hi,

    I have a transcriptome assembly that is comprised of a metazoan and protist (intracellular symbiont) component. I know from the assemblies of similar organisms that the CG percentage of the two organisms are very different and can be used to separate contigs.

    Is there a simple tool that I can use to (1) determine the GC content (%) of each contig in the final assembly (fasta) and (2) plot the histogram (or provide the bins for plotting) and (3) split the fasta file based on GC content (or provide a list of contigs with associated GC % that can be sorted and split).

    I suppose 2 and 3 are a bit redundant because I can plot the histogram from the list of contigs and GC %.

    Thanks,
    Dave

  • #2
    Hi Dave,

    The BBMap package has a tool called Stats (stats.sh) which will list the gc content per scaffold to a file like this:

    Code:
    stats.sh in=assembly.fa gc=gc.txt
    You can plot a histogram and subsequently bin like this:

    Code:
    reformat.sh in=assembly.fa gchist=gchist.txt
    reformat.sh in=assembly.fa out=low.fa maxgc=0.45
    reformat.sh in=assembly.fa out=high.fa mingc=0.450001

    Comment


    • #3
      Originally posted by Brian Bushnell View Post
      Hi Dave,

      The BBMap package has a tool called Stats (stats.sh) which will list the gc content per scaffold to a file like this:
      I must admit I was hoping and, quite frankly, expecting, that BBMap would be capable of this. Once again thank you for your excellent package...

      Yours,
      Dave

      Comment

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