After performing a novo assembly, with the followed command, i want to filter the biggest 50 contigs.
spades.py --untrusted-contigs lclav_genome.fa -1 randomnietnfectedFP.fastq.gz -2 randomnietinfectedRP.fastq.gz -t 2 -m 28 NINnovo --phred-offset 33
This creates a directory with the contigs in it. This file is sorted from biggest to smallest, and we want just the top 50 of these contigs. I have tried something with awk, but it is not working how i want it to. CAn someone help me out?