Assembly QC

Basic statistics

You can run assembly-stats to get basic statistics like N50, assembly size and number of contigs:

assembly-stats contigs.fa

You can run infoseq to get a breakdown of contigs, their lengths and GC%:

infoseq -auto -only -accession -length -pgc contigs.fa


Quast is a useful way of performing assembly QC, particularly if you have some kind of reference genome to compare against.