To compile: g++ -o outputfile -O3 Source.cpp
To use:
AssemblyStatistics: ./AssemblyStatistics contigs YourAssembly.fasta or ./AssemblyStatistics contigs [YourAssembly.fasta] GS [Estimated_Genome_Size]
SelectLongestReads: longest 0: select the first reads that sum to total_length bases. longest 1: select the longest reads that sum to total_length bases. ./SelectLongestReads sum [total_length] longest [0 or 1] o [outfile] f [fa/fq_file] f [fa/fq_file] "