GC content of assembled transcripts

[DrYak]

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

[Brian Bushnell]

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:

stats.sh in=assembly.fa gc=gc.txt

You can plot a histogram and subsequently bin like this:

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

[DrYak]

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