where **input_reads_pair_1.[fa|fq]** and **input_reads_pair_2.[fa|fq]** are the input paired-end files of sequence reads in fasta/fastq format, and **--seqType** is the type of these input reads. The option **--JM** defines the number of GB of system memory required for k-mer counting by jellyfish.
where **input_reads_pair_1.[fa|fq]** and **input_reads_pair_2.[fa|fq]** are the input paired-end files of sequence reads in fasta/fastq format, and **--seqType** is the type of these input reads. The option **--max_memory** specifies the maximum memory to use with Trinity.
Additional Trinity **options** can be found in the Trinity website, or by typing: