Writing a script for quast
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.
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babdalhamid •
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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.
Hello babdalhamid,
Please use the formatting bar (especially the
codeoption) to present your post better. I've done it for you this time.Thank you!
See a similar post
A: How to run a set or batch of genome assemblies at once in one go?