spades.py --pe1-1 <sample.R1.fastq> --pe1-2 <sample.R2.fastq> -o <output_dir>

VelvetOptimiser.pl -f "-shortPaired -fastq -separate sample.R1.fastq sample.R2.fastq" \
                   -s <starting_hash_value> \
                   -e <end_hash_value> \
                   -d <output_dir>

soapdenovo all -s <config_file> -K <K-mer_size> -R -o <graph_prefix>

canu -p <assembly-prefix> \
     -d <assembly-directory> \
     genomeSize=<genome_size> \
     -nanopore <sample_guppy.fastq>

necat.pl config <sample_config.txt>
necat.pl correct <sample_config.txt>
necat.pl assemble <sample_config.txt>
necat.pl bridge <sample_config.txt>

quast.py <scaffolds.fasta> -o <output>

busco -i <SEQUENCE_FILE> -l <LINEAGE> -o <OUTPUT_NAME> -m <genome>