GemReads requires as input an error model file (generated by users with GemErr or supplied in GemSIM), a FASTA genome file or directory of FASTA genomes (metagenomics mode), an optional haplotype file (user defined or from GemHaps), and a tab-delimited species-abundance text file (metagenomics mode only). Additionally, the user specifies whether the reference genome(s) are circular or linear, and which quality score offset to use (33 or 64, depending on the required FASTQ output version). The requested number of single or paired-end reads are generated as follows, and output as FASTQ files:
