How do I use Quast to produce quality metrics of multiple contig files at once
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2.2 years ago
dikisakye • 0

I have performed denovo assembly on cryptococcus neoformans genomes from multiple samples. I now have the contig files for these assemblies and would want to compute the quality metrics using quast. I want to create a script that loops over each contig file to compute the metrics and puts the outputs all results into a separate results directory. Can someone guide me on how to do this?. This is my directory structure:

Samples | +-- sample1 | |
| +-- sample1_contigs.fa |
+-- sample2 | |
| +-- sample2_contigs.fa |
|
+-- sample3 | | | +--sample3_contigs.fa | +-- sample4 etc

assembly statistics quast Genome • 408 views
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