text: user10594: I am analysing Pyrococcus Furiosus DNA sequencing data by considering data published here in NCBI. When I click on "Send to">"Gene Features">"FASTA format" I download a file that has the sequences of genes of this organism but I realized that this file has some sequences that are doubled (that is the sequence is present twice with different identifiers)... is there a way to get a file with all genes annotated and their respective DNA sequences without double sequences and with all sequences in the 5' to 3' direction without reverse complement in a well "ordered" way ? In NCBI (in the link I reported before) it indicates 2,128 genes so I would like a file with all these 2,128 genes annotated and their respective DNA sequences in FASTA format. Do you know if there is an other website or an other place in NCBI in which I can search to get this kind of file?
  EDIT: if you follow the path "Send to">"Gene Features">"FASTA format", now it seems that there are just 2,128 genes so this problem is vanished in this case. Anyway, I would appreciate the answer for the future and for the reverse complement gene sequences that are still there.
  Thank you very much.
  
  user6628: From this SO post. You can use seqkit to remove duplicate sequences with the command below:
  seqkit rmdup -s < sequences.txt > out.fa
  
  
  The rmdup option removes duplicates, and the -s option calls duplicates on the basis of sequence, ignoring differences in headers.
  
  
original_text: 10594: <p>I am analysing Pyrococcus Furiosus DNA sequencing data by considering data published <a href="https://www.ncbi.nlm.nih.gov/nuccore/NC_003413.1" rel="nofollow noreferrer">here</a> in NCBI. When I click on &quot;Send to&quot;&gt;&quot;Gene Features&quot;&gt;&quot;FASTA format&quot; I download a file that has the sequences of genes of this organism but I realized that this file has some sequences that are doubled (that is the sequence is present twice with different identifiers)... is there a way to get a file with all genes annotated and their respective DNA sequences without double sequences and with all sequences in the 5' to 3' direction without reverse complement in a well &quot;ordered&quot; way ? In NCBI (in the link I reported before) it indicates 2,128 genes so I would like a file with all these 2,128 genes annotated and their respective DNA sequences in FASTA format. Do you know if there is an other website or an other place in NCBI in which I can search to get this kind of file?</p>
  <p>EDIT: if you follow the path &quot;Send to&quot;&gt;&quot;Gene Features&quot;&gt;&quot;FASTA format&quot;, now it seems that there are just 2,128 genes so this problem is vanished in this case. Anyway, I would appreciate the answer for the future and for the reverse complement gene sequences that are still there.</p>
  <p>Thank you very much.</p>
   6628: <p>From <a href="https://stackoverflow.com/a/61374803/7092484">this SO post</a>. You can use <a href="https://bioinf.shenwei.me/seqkit/" rel="nofollow noreferrer">seqkit</a> to remove duplicate sequences with the command below:</p>
  <pre><code>seqkit rmdup -s &lt; sequences.txt &gt; out.fa
  </code></pre>
  <blockquote>
  <p>The <code>rmdup</code> option removes duplicates, and the <code>-s</code> option calls duplicates on the basis of sequence, ignoring differences in headers.</p>
  </blockquote>
  