Question

How to get general information of an assembly

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6.5 years ago

luzglongoria ▴ 50

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 • 2.0k views

ADD COMMENT • link updated 6.5 years ago by Buffo ★ 2.5k • written 6.5 years ago by luzglongoria ▴ 50

score 2 · Accepted Answer · 2019-04-23

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6.5 years ago

Sej Modha 5.3k

You could try transrate or rnaQUAST

ADD COMMENT • link 6.5 years ago by Sej Modha 5.3k

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Thank you for the quick response :)

Do they support .fa files?

ADD REPLY • link 6.5 years ago by luzglongoria ▴ 50

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

ADD REPLY • link 6.5 years ago by Sej Modha 5.3k

score 2 · Accepted Answer · 2019-04-23

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6.5 years ago

Buffo ★ 2.5k

You can also check biopieces:

read_fasta -i assembly.fasta | analyze_assembly -x

ADD COMMENT • link 6.5 years ago by Buffo ★ 2.5k