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 .
