If you want to do it CLI, there is a program called bioawk (see here) that can do this job easily!
bioawk -c fastx 'length($seq) >200 {print $name"\n"$seq}' scaffolds.fasta
if you want to print it pretty, then pipe it through fold command!
here, -c is for specifying the input file type (fastx for fasta, fastq etc)
filtering criteria is specified as length($seq) >200 which is straight forward
and to print the fasta sequence back print $name"\n"$seq}
Hope this helps!
This command line leaves the sequence names without ">" what corrupts the file. Just modify according to bioawk example:
bioawk -c fastx 'length($seq) >200 {print ">"$name"\n"$seq}' scaffolds.fasta
If you have limited bioinformatics skills, I recommend using Bioedit. With it you can sort your contigs by length, and manually exclude those not desirable. Otherwise, you can use this fantastic toolkit: FAST (https://github.com/tlawrence3/FAST).
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