Main tool : seqyclean
Seqyclean "cleans" NGS sequencing data. A file containing Illumina adapaters and PhiX is located at /Adapters_plus_PhiX_174.fasta.
seqyclean -minlen 25 -qual -c /Adapters_plus_PhiX_174.fasta -1 {reads.R1.fastq.gz} -2 {reads.R2.fastq.gz} -o Sequencing_reads/QCed/{sample}_clean