text: user16329: My goal is to compare reads from two different fastq files on a Linux machine.
  The following are the comparisons to perform:
  
  How many common reads are between the two fastq files?
  How many reads are present in one fastq file that are not present in the other? i.e reads that are unique to each file.
  Where and how do the sequences differ in both files? Is there a difference in nucleotide base at the end of the sequence(3' end), the start of the sequence(5'end) or is it somewhere in the middle of the sequence? Is there a difference in length of the sequence? If so, what is the length and what is the difference? I would like to get the original sequences plus the difference between them for analysis.
  Does the quality score differ? Where and how do the quality of sequences differs?
  
  Any guidance regarding how to approach this question is very appreciated.
  Edit: I'm working on paired-end reads from the same individual. What I want to do is to compare different trimming tools from their output.
  
  user2245: There are several things you can try. For example, Simka (https://github.com/GATB/simka) is tool that compares the profiles of the genomic content of fastq files and generates several types of plots e.g. heatmap.
  Another tool that might be useful is multifastqc (https://multiqc.info/), which aggregates results and has multiple options.
  
original_text: 16329: <p>My goal is to compare reads from two different fastq files on a Linux machine.
  The following are the comparisons to perform:</p>
  <ol>
  <li>How many common reads are between the two fastq files?</li>
  <li>How many reads are present in one fastq file that are not present in the other? i.e reads that are unique to each file.</li>
  <li>Where and how do the sequences differ in both files? Is there a difference in nucleotide base at the end of the sequence(3' end), the start of the sequence(5'end) or is it somewhere in the middle of the sequence? Is there a difference in length of the sequence? If so, what is the length and what is the difference? I would like to get the original sequences plus the difference between them for analysis.</li>
  <li>Does the quality score differ? Where and how do the quality of sequences differs?</li>
  </ol>
  <p>Any guidance regarding how to approach this question is very appreciated.</p>
  <p>Edit: I'm working on paired-end reads from the same individual. What I want to do is to compare different trimming tools from their output.</p>
   2245: <p>There are several things you can try. For example, Simka (<a href="https://github.com/GATB/simka" rel="nofollow noreferrer">https://github.com/GATB/simka</a>) is tool that compares the profiles of the genomic content of fastq files and generates several types of plots e.g. heatmap.</p>
  <p>Another tool that might be useful is <a href="https://multiqc.info/" rel="nofollow noreferrer">multifastqc</a> (<a href="https://multiqc.info/" rel="nofollow noreferrer">https://multiqc.info/</a>), which aggregates results and has multiple options.</p>
  