Dear all, 

I am new to the field. I am trying to analyze single end 100b FastQ files with ~70million reads/sample.  I am trying to determine if adapter sequences are present and if so how to go about them. I ran FastQC on the files and reports show they each have an "overrepresented sequence" of an "illumina index adapter" in them.

<a href="https://ibb.co/R6N3Nr5"><img src="https://i.ibb.co/pKQfQVm/sample1.png" alt="sample1" border="0" /></a>


I have the following questions:
 
1. Does sample1 look like a trimmed file or it requires adapter trimming?
 
2. If further trimming is recommended what would be the best seq/adapter option to be used for cutadapt/TrimGalore? [See below for my thoughts so far] 

3. Based on the FastQC report, do I need to worry about presence of any other adapter sequences beside the index?  

My thoughts on question 2: 
The sequences for illumina index adapter format appear to be:  

    GATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG

 

 These are the adapter sequences found in my FastQC report for sample 1: 

    GATCGGAAGAGCACACGTCTGAACTCCAGTCACCATGGCATCTCGTATGC 
    AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCATGGCATCTCGTATG 

I am thinking of using below options for cutadapt/trimgalore to remove the adapter(s): 

    trim_galore sample1.fastq.gz -a GATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -q 20 --length 20 –fastqc 

However, it seems that trimmomatics for instance only takes care of the initial sequence of the index adapter (only up to Ns and not after): 
https://github.com/timflutre/trimmomatic/blob/master/adapters/TruSeq3-SE.fa 

Many thanks for your time and reply beforehand.
The sequence to trim if having Universal Adaprer contaminations is `AGATCGGAAGAGC`.
In you case (0.5%) I would not even bother and directly align the files without any manipulations. 