Question: Writing a script for quast
0
gravatar for babdalhamid
17 months ago by
babdalhamid0 wrote:

I am running spades for denovo assembly for several strains. I want to run quast for quality check on denovo assembly using the following command

quast.py contigs.fasta

I want to write a script like looping (while) so I do not need to manually enter the command each time. contigs.fasta is found in the output directory of spades denovo assembly. I want quast to:

  • 1- Read contigs.fasta in each assembly directory separately.

  • 2- To create a table that contain a list of all assembly information for each strain in one table only.

assembly • 1.0k views
ADD COMMENTlink modified 9 months ago by zx87549.4k • written 17 months ago by babdalhamid0

You can write either a bash loop or parallel to run quast for point 1. For point 2, I guess quast outputs a summary table and summary graph. You can parse it as per your requirements. babdalhamid. Please post the example directory tree/structure.

ADD REPLYlink written 17 months ago by cpad011213k

See a similar post

A: How to run a set or batch of genome assemblies at once in one go?

ADD REPLYlink written 17 months ago by lakhujanivijay5.1k
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