Basic Illumina Sequence Quality Control
Assess raw FASTQ sequences using the program FastQCGoal.
Remove low quality sequences to increase average quality score of reads above 28 For current sequencing centers, the 5' end of has had Illumina adapters and primers removed.
But there can be inclusion of the 3' end Illumina adapter in DNA fragments with length less than the number of the cycles for the sequencer.
Remove Illumina adaptor sequences from 3' end of sequences - be sure to preserve reads of 0 length.
Repeat step for all raw read files.
Assess Cutadapt results with FastQC.
Remove low quality base pairs from sequences, generally from the 3' end, using a sliding window of 10 bp that will trim all trailing bases if the average quality score drops below 28.
Important: To maintain the order of paired-end Illumina sequences both reads must be input simultaneously with the same number of sequences submitted from each read pair, regardless of the length of the sequence.
Assess file quality scores using FastQC.
Utilize Trimmomatic for any other issues - such as poor quality in the first bp, etc.
