How to get general information of an assembly

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!

rna-seq assembly software

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updated 7.3 years ago by Buffo

• written 7.3 years ago by luzglongoria •

2 answers

You could try transrate or rnaQUAST

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written 7.3 years ago by Sej Modha

Thank you for the quick response :)

Do they support .fa files?

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written 7.3 years ago by luzglongoria •

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

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written 7.3 years ago by Sej Modha

You can also check biopieces:

read_fasta -i assembly.fasta | analyze_assembly -x

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written 7.3 years ago by Buffo

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