text: user2381: I am working on ONT data. Initially, I have worked on data from 1D using Minimap2 aligner. I came across 1D^2 from ONT website. I was wondering how different is the data from two techniques? What is the difference between 1D and 2D? and do we get 2  fastq files (one per strand) for each sample? 
  TIA
  I would greatly appreciate any help regarding my question. 
  
  user73: 1D² data that is called by Albacore generates two overlapping sets of files. Here's what Devon O'Rourke mentioned on the ONT community forums and on Twitter:
  
  Following Albacore basecalls on a 1d2 library I get two sets of .fq files, summary stats, etc.: one for the 1D basecalling script, and one for the 1D2 script. I'd like to use the reads generated from these scripts in a genome assembly.
  After a little bit of grep searching, it seems like there are overlapping reads among the 1D and 1D2 directories - namely, those 1d reads that generated 1d2 reads!
  
  Link here, for those who have ONT community access.
  I've recommended generating a list of the 1D^2 reads, then excluding those reads from the 1D fastq files. I have a couple of scripts that can help for this:
  $ cat 1d2_reads.fq | ~/scripts/fastx-length.pl | perl -lane '$F[1] =~ s/(.{36})/$1\n/; print $F[1];' > readNames.txt
  $ cat 1d_reads.fq | ~/scripts/fastx-fetch.pl -v -i readNames.txt > filtered_1d_reads.fq
  
  More information on this can also be found in this StackExchange answer.
  
original_text: 2381: <p>I am working on ONT data. Initially, I have worked on data from 1D using Minimap2 aligner. I came across 1D^2 from ONT website. I was wondering how different is the data from two techniques? What is the difference between 1D and 2D? and do we get 2  fastq files (one per strand) for each sample? </p>
  
  <p>TIA</p>
  
  <p>I would greatly appreciate any help regarding my question. </p>
   73: <p>1D² data that is called by Albacore generates two overlapping sets of files. Here's what Devon O'Rourke mentioned on the ONT community forums and on Twitter:</p>
  
  <blockquote>
    <p>Following Albacore basecalls on a 1d2 library I get two sets of .fq files, summary stats, etc.: one for the 1D basecalling script, and one for the 1D2 script. I'd like to use the reads generated from these scripts in a genome assembly.</p>
    
    <p>After a little bit of <code>grep</code> searching, it seems like there are overlapping reads among the 1D and 1D2 directories - namely, those 1d reads that generated 1d2 reads!</p>
  </blockquote>
  
  <p>Link <a href="https://community.nanoporetech.com/posts/albacore-1d2-output-direct" rel="nofollow noreferrer">here</a>, for those who have ONT community access.</p>
  
  <p>I've recommended generating a list of the 1D^2 reads, then excluding those reads from the 1D fastq files. I have a <a href="https://github.com/gringer/bioinfscripts/blob/master/fastx-length.pl" rel="nofollow noreferrer">couple</a> of <a href="https://github.com/gringer/bioinfscripts/blob/master/fastx-fetch.pl" rel="nofollow noreferrer">scripts</a> that can help for this:</p>
  
  <pre><code>$ cat 1d2_reads.fq | ~/scripts/fastx-length.pl | perl -lane '$F[1] =~ s/(.{36})/$1\n/; print $F[1];' &gt; readNames.txt
  $ cat 1d_reads.fq | ~/scripts/fastx-fetch.pl -v -i readNames.txt &gt; filtered_1d_reads.fq
  </code></pre>
  
  <p>More information on this can also be found in <a href="https://bioinformatics.stackexchange.com/questions/3333/removing-repeated-reads-from-nanopore-1d%C2%B2-reads">this StackExchange answer</a>.</p>
  