Writing a script for quast

Question

[babdalhamid]

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.

[cpad0112]

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.

[lakhujanivijay]

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