Take a look to BBDuk. There is plenty of information about it HERE

You can try Trim_galore http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/:

Single end

trim_galore $phred --fastqc --illumina --clip_R1 3 --clip_R2 3 $read[0] --output_dir ../fastq_trim

Pair-end

trim_galore $phred --fastqc --illumina --paired --clip_R1 3 --clip_R2 3 --three_prime_clip_R1 3 --three_prime_clip_R2 3 $read[0] $read[1] --output_dir ../

If you are removing the Nextera internal adapter for mate-pair libraries, you should use NxTrim:

https://github.com/sequencing/NxTrim

This will both trim the internal adapter and categorize the reads into groups: true mate-pairs, single-end, paired-end, and unknown (no adapter found, so likely a mix of true mates and paired-end). Note that the tool will revcomp the output by default to make them innies, which is NOT what most assemblers want. You can stifle this to keep the outie orientation by using the --norc option.

Otherwise, the above choices will work for other standard adapter sequences.