text: user9912: I am using count_overlap() for counting the kmers from Biopython .
  Does it take the reverse complement of kmer into account?
  I need to count reverse complement too
  
  user3848: There's a lot detail missing here, but at a guess could you try,
  from Bio import SeqIO
  from Bio.Seq import Seq
  for record in SeqIO.parse("ls_orchid.gbk", "genbank"):
      reversec = record.seq.reverse_complement())
      revcount = reversec.count_overlap('AT')
      print (revcount + count_overlap('AT'))
  
  Essentially count_overlap only counts the forward strand if this is the Biopython method. Not debugged the above.
  
  user776: Here's a C++ kmer counter I wrote for my own purposes. It can count canonical and reverse complement kmers from FASTA files up to length 31. Run kmer-counter --help or read the README for count options.
  For longer kmers, you'd want to look at an approximation tool like Jellyfish.
  
original_text: 9912: <p>I am using count_overlap() for counting the kmers from Biopython .</p>
  <p>Does it take the reverse complement of kmer into account?</p>
  <p>I need to count reverse complement too</p>
   3848: <p>There's a lot detail missing here, but at a guess could you try,</p>
  <pre><code>from Bio import SeqIO
  from Bio.Seq import Seq
  for record in SeqIO.parse(&quot;ls_orchid.gbk&quot;, &quot;genbank&quot;):
      reversec = record.seq.reverse_complement())
      revcount = reversec.count_overlap('AT')
      print (revcount + count_overlap('AT'))
  </code></pre>
  <p>Essentially <code>count_overlap</code> only counts the forward strand if this is the Biopython method. Not debugged the above.</p>
   776: <p><a href="https://github.com/alexpreynolds/kmer-counter" rel="nofollow noreferrer">Here's a C++ kmer counter</a> I wrote for my own purposes. It can count canonical and reverse complement kmers from FASTA files up to length 31. Run <code>kmer-counter --help</code> or read the README for count options.</p>
  <p>For longer kmers, you'd want to look at an approximation tool like <a href="https://github.com/gmarcais/Jellyfish" rel="nofollow noreferrer">Jellyfish</a>.</p>
  