text: user-1: I want to remove reads from FASTQ file that contain homopolymers > 10bp and remove reads with <35 average quality score across the entire read.
  To remove homopolymers > 10bp, I tried this on a Linux machine, but it only removes the sequence line:
  zcat file.fastq.gz | 
    awk '!/A{10,}/&&!/C{10,}/&&!/G{10,}/&&!/T{10,}/ {print}' cleaned_file.fastq
  
  
  user2108: Use an off the shelf tool for read preprocessing.
  Here is one:
  ./fastq_qual_trimmer -i test.fq -m 35 -H 10
  
  That one does exactly what you want but seems a little old/unmaintained, so here is another that does more or less the same thing:
  fastq-mcf --qual-mean 35 --homopolymer-pct {X} adapters.fa reads.fq
  
  where {X} is 10 / read length, adapters.fa is an adapter file (which I believe can be empty or filled with dummy sequences).
  You could also use a library like biopython or dnaio to write a quick script to do this, but it hardly seems worth it.
  
original_text: -1: <p>I want to remove reads from FASTQ file that contain homopolymers &gt; 10bp and remove reads with &lt;35 average quality score across the entire read.</p>
  <p>To remove homopolymers &gt; 10bp, I tried this on a Linux machine, but it only removes the sequence line:</p>
  <pre><code>zcat file.fastq.gz | 
    awk '!/A{10,}/&amp;&amp;!/C{10,}/&amp;&amp;!/G{10,}/&amp;&amp;!/T{10,}/ {print}' cleaned_file.fastq
  </code></pre>
   2108: <p>Use an off the shelf tool for read preprocessing.</p>
  <p><a href="https://github.com/ivars-silamikelis/fastq_qual_trimmer" rel="nofollow noreferrer">Here is one</a>:</p>
  <pre><code>./fastq_qual_trimmer -i test.fq -m 35 -H 10
  </code></pre>
  <p>That one does exactly what you want but seems a little old/unmaintained, so here is <a href="https://manpages.debian.org/testing/ea-utils/fastq-mcf.1.en.html" rel="nofollow noreferrer">another</a> that does more or less the same thing:</p>
  <pre><code>fastq-mcf --qual-mean 35 --homopolymer-pct {X} adapters.fa reads.fq
  </code></pre>
  <p>where <code>{X}</code> is 10 / read length, adapters.fa is an adapter file (which I believe can be empty or filled with dummy sequences).</p>
  <p>You could also use a library like biopython or dnaio to write a quick script to do this, but it hardly seems worth it.</p>
  