text: user3772: Dealing whith a problematic sequencing run I found this over-represented sequence:
  
  GGAAGAGCACACGTCTGAACTCCAGTCACTAGCTTATCTCGTATGGCGTCTTCTGCTTG
  
  It is clearly relate to the Illumina sequencing primer as shown by this read structure description (note the bold residues above):
  
  I searched the sequence in the nucleotide NR ncbi database, using blastn (standard parameters) and I found this as a first hit:
  Severe acute respiratory syndrome coronavirus 2 genome assembly, chromosome: 1
  Sequence ID: OV196492.1Length: 30243Number of Matches: 2
  Range 1: 73 to 133GenBankGraphicsNext MatchPrevious Match
  Alignment statistics for match #1
  Score   Expect  Identities  Gaps    Strand
  89.8 bits(48)   2e-14   57/61(93%)  2/61(3%)    Plus/Minus
  Query  1    GGAAGAGCACACGTCTGAACTCCAGTCACTAG--CTTATCTCGTATGGCGTCTTCTGCTT  58
              ||||||||||||||||||||||||||||| ||  ||||||||||||| ||||||||||||
  Sbjct  133  GGAAGAGCACACGTCTGAACTCCAGTCACCAGTGCTTATCTCGTATGCCGTCTTCTGCTT  74
  
  Query  59   G  59
              |
  Sbjct  73   G  73
  
  
  Range 2: 188 to 248GenBankGraphicsNext MatchPrevious MatchFirst Match
  Alignment statistics for match #2
  Score   Expect  Identities  Gaps    Strand
  89.8 bits(48)   2e-14   57/61(93%)  2/61(3%)    Plus/Minus
  Query  1    GGAAGAGCACACGTCTGAACTCCAGTCACTAG--CTTATCTCGTATGGCGTCTTCTGCTT  58
              ||||||||||||||||||||||||||||| ||  ||||||||||||| ||||||||||||
  Sbjct  248  GGAAGAGCACACGTCTGAACTCCAGTCACCAGTGCTTATCTCGTATGCCGTCTTCTGCTT  189
  
  Query  59   G  59
              |
  Sbjct  188  G  188
  
  There are also sequences of other virues that match very well.
  Do you know what is the relation between Illumina adapters/primers and viral seqiuences?
  
  user77: You'll unfortunately find adapter sequences contaminating a lot of entries in Genbank. In short, the sequence is most likely either an unassembled fragment where the input into the assembly step hadn't had adapters trimmed or (somewhat more rarely) the adapter sequence was incorporated into an assembled contig and then uploaded. You'll see a lot of lower quality sequences like this, especially from massive viral screens.
  Be aware that there are other quality issues facing particularly virus sequences such as extremely high NNN stretches (cf. the difficulties faced in creating the C-RVDB viral database once there were hundreds of thousands of apparently poor-quality coronavirus sequences automatically added to Genbank).
  
original_text: 3772: <p>Dealing whith a problematic sequencing run I found this over-represented sequence:</p>
  <blockquote>
  <p><strong>GGAAGAGCACACGTCTGAACTCCAGTCAC</strong>TAGCTT<strong>ATCTCGTATGGCGTCTTCTGCTTG</strong></p>
  </blockquote>
  <p>It is clearly relate to the Illumina sequencing primer as shown by this read structure description (note the bold residues above):</p>
  <p><a href="https://i.stack.imgur.com/oL4Sr.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/oL4Sr.png" alt="illumina primers" /></a></p>
  <p>I searched the sequence in the nucleotide NR ncbi database, using blastn (standard parameters) and I found this as a first hit:</p>
  <pre><code>Severe acute respiratory syndrome coronavirus 2 genome assembly, chromosome: 1
  Sequence ID: OV196492.1Length: 30243Number of Matches: 2
  Range 1: 73 to 133GenBankGraphicsNext MatchPrevious Match
  Alignment statistics for match #1
  Score   Expect  Identities  Gaps    Strand
  89.8 bits(48)   2e-14   57/61(93%)  2/61(3%)    Plus/Minus
  Query  1    GGAAGAGCACACGTCTGAACTCCAGTCACTAG--CTTATCTCGTATGGCGTCTTCTGCTT  58
              ||||||||||||||||||||||||||||| ||  ||||||||||||| ||||||||||||
  Sbjct  133  GGAAGAGCACACGTCTGAACTCCAGTCACCAGTGCTTATCTCGTATGCCGTCTTCTGCTT  74
  
  Query  59   G  59
              |
  Sbjct  73   G  73
  
  
  Range 2: 188 to 248GenBankGraphicsNext MatchPrevious MatchFirst Match
  Alignment statistics for match #2
  Score   Expect  Identities  Gaps    Strand
  89.8 bits(48)   2e-14   57/61(93%)  2/61(3%)    Plus/Minus
  Query  1    GGAAGAGCACACGTCTGAACTCCAGTCACTAG--CTTATCTCGTATGGCGTCTTCTGCTT  58
              ||||||||||||||||||||||||||||| ||  ||||||||||||| ||||||||||||
  Sbjct  248  GGAAGAGCACACGTCTGAACTCCAGTCACCAGTGCTTATCTCGTATGCCGTCTTCTGCTT  189
  
  Query  59   G  59
              |
  Sbjct  188  G  188
  </code></pre>
  <p>There are also sequences of other virues that match very well.</p>
  <p>Do you know what is the relation between Illumina adapters/primers and viral seqiuences?</p>
   77: <p>You'll unfortunately find adapter sequences contaminating a lot of entries in Genbank. In short, the sequence is most likely either an unassembled fragment where the input into the assembly step hadn't had adapters trimmed or (somewhat more rarely) the adapter sequence was incorporated into an assembled contig and then uploaded. You'll see a lot of lower quality sequences like this, especially from massive viral screens.</p>
  <p>Be aware that there are other quality issues facing particularly virus sequences such as extremely high NNN stretches (cf. the difficulties faced in creating the C-RVDB viral database once there were hundreds of thousands of apparently poor-quality coronavirus sequences automatically added to Genbank).</p>
  