Parameter	Explanation
-a C{12}N{38}	In a sequence of 12 cytidines in a row, remove everything including and 3′ to that motif. The N{38} captures additional nucleotides 3′ to the poly(C) motif, up to a 51-nt read. If using shorter or longer sequencing cycle data, adjust the number accordingly.
-m 18 -M 76	Discards reads shorter than 18 bp and longer than 76 bp. If using shorter or longer sequencing cycle data, adjust the -M number accordingly.
-j 4	Uses four logical threads for trimming; speeds execution of the program. Can set it lower if limited by hardware.
-trim-n	Removes ambiguous nucleotides from the ends of reads.
-o FILENAME_Trimmed.fastq.gz	This is the name of the outputted trimmed reads, in fastq.gz file format. Replace “FILENAME” with the desired name.
FILENAME.fastq.gz	Replace “FILENAME” with the name of the raw sequencing read file obtained from the sequencing core facility.