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
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
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