How to get general information of an assembly

Question

[luzglongoria]

Hi there,

I have done my assembly with Trinity and I would like to know whether is there any software for getting general info about the assembly. I would like to know:

Number of bases (total number) Contig length min-max (bp) Median contig length (bp) Mean contig lenghth (bp)

do you know any software that I can use for this purpose?

thank you in advance!

Answer 1

[Sej Modha]

You could try transrate or rnaQUAST

[luzglongoria]

Thank you for the quick response :)

Do they support .fa files?

[Sej Modha]

They should do, please refer to the manual for more info.

Answer 2

[Buffo]

You can also check biopieces:

read_fasta -i assembly.fasta | analyze_assembly -x