Plot distribution of length of sequences

[noha osman]

Hi all

I have 72 fasta files and I would like to do plot distribution to check sequence length of those files

Is there any tool to do that?

Can you suggest me something also a little script please?

Thanks

[Brian Bushnell]

BBTools has a few scripts for plotting the length distribution of reads:

readlength.sh in=file out=histogram.txt bin=10 max=80000

That will plot the result in bins of size 10, with everything above 80k placed in the same bin. The defaults are set for relatively short sequences so if they are many megabases long you may need to add the flag "-Xmx8g" and increase "max=" to something much higher.

Alternatively, if these are assemblies and you're interested in continuity information (L50, N50, etc), you can run stats on each or statswrapper on all of them:

stats.sh in=file

or

statswrapper.sh in=file,file,file,file...