Thanks to @mbhall88 the functionality of --ignore has been extended If your input FASTA or GFA is mixed (e.g. has chromosome and plasmids), you can also use dnaapler all, with the option to ignore some contigs with the --ignore parameter. The --ignore parameter now accepts either: A file path containing contig names to ignore (one per line) A comma-separated list of contig names (e.g., chr1,chr2,chr3) to read contig names from stdin (one per line) using - e.g. dnaapler all -i input.fasta -o output_directory_path -p my_genome_name --ignore list_of_contigs_to_ignore.txt dnaapler all -i input.fasta -o output_directory_path -p my_genome_name --ignore chr1,chr2,chr3 echo -e "chr1\nchr2\nchr3" | dnaapler all -i input.fasta -o output_directory_path -p my_genome_name --ignore -