text: user9104: I had a question for the community.
  I have a genome of a new species that has been sequenced via 150pb Illumina paired-end.
  To verify the quality of the assembly I used the BUSCO pipeline which allows me to search for 99% of the BUSCO genes (gene not duplicated) present in a taxon in the genome of my species.
  Globally I only miss 18% of the BUSCO genes, which means that the assembly is not too bad.
  Now when I plot the G+C% and the coverage of all the scaffolds containing BUSCO genes (so a priori non-contaminating) I should find a fairly homogeneous cloud.
  Instead I end up with two different coverage profiles (noted red and blue below):
  
  I then thought that the low coverage sequencing profile around 4x might be a eukaryotic contaminant like a acarians, however when I blast the BUSCOs present on these low coverage scaffolds I get hits that are very close to the genome of my species...
  Does anyone have any idea what these are?
  here is an output of the contigsTable.csv where the two first row are scaffold with low coverage in the figure, and two last are scaffold with high coverage in the figure
  
  FRC output
  
  Coverage distribution
  
  Here is an Icarus summary of the assembly :
  Assembly
  # contigs (>= 0 bp) 1038631
  # contigs (>= 1000 bp) 120132
  # contigs (>= 5000 bp) 22245
  # contigs (>= 10000 bp) 9986
  # contigs (>= 25000 bp) 1322
  # contigs (>= 50000 bp) 97
  Total length (>= 0 bp) 655530043
  Total length (>= 1000 bp) 451497861
  Total length (>= 5000 bp) 260894112
  Total length (>= 10000 bp) 174183054
  Total length (>= 25000 bp) 45006012
  Total length (>= 50000 bp) 5956145
  # contigs 214542
  Largest contig 120620
  Total length 519138286
  GC (%) 32.94
  N50 5062
  N75 1624
  L50 21982
  L75 71030
  # N's per 100 kbp 22.28
  
  Here is the BUSCO summary as well :
  2544 Complete BUSCOs (C)
  2312 Complete and single-copy BUSCOs (S)
  232 Complete and duplicated BUSCOs (D)
  1060 Fragmented BUSCOs (F)
  811 Missing BUSCOs (M)
  4415 Total BUSCO groups searched
  C:57.7%[S:52.4%,D:5.3%],F:24.0%,M:18.3%,n:4415
  
  EDIT
  I ran the fastq sequences with another aligner (MEGAHIT) to see if it was not because of an assembly issue and I got the same profils coverage see here :
  
  
  user9693: This could be organism-specific. We don't have a lot of info so far, so I would check a few more things:
  Run something like FRC_align. Check if there's a clear signal between regions flagged as suspicious by it and your coverage graph.
  Is it a eukaryote? Plant? Check where mitchondria and chloroplasts are on the plot. They will have different GC/coverage signals than the rest of your assembly, which is fine, expected even.
  Worried about contamination? Run kraken2 on your raw data and see what you get there.
  Run RepeatMasker and check if repetive regions contribute to the effect you see.
  Finally, unless your specimen is low heterozygosity, haploid, or inbred, you probably have some effect from ploidy. There are numerous ways to check that. A self-self dot plot with MUMmer and looking coverage histograms are a good start. The idea is that you should see two peaks (let's assume diploid). One for the split haplotigs, and one for collapsed.
  I checked the GC distribution of 45 genomes in your order. It's kind of all over the place, but there are some bimodal ones:
  
  What does GC vs Length look like? Here's the one from the 45 genomes mentioned above:
  
  
original_text: 9104: <p>I had a question for the community.</p>
  <p>I have a genome of a new species that has been sequenced via 150pb Illumina paired-end.</p>
  <p>To verify the quality of the assembly I used the <code>BUSCO pipeline</code> which allows me to search for 99% of the BUSCO genes (gene not duplicated) present in a taxon in the genome of my species.</p>
  <p>Globally I only miss <code>18%</code> of the BUSCO genes, which means that the assembly is not too bad.</p>
  <p>Now when I plot the <strong>G+C%</strong> and the <strong>coverage</strong> of all the scaffolds containing BUSCO genes (so a priori non-contaminating) I should find a fairly homogeneous cloud.</p>
  <p>Instead I end up with two different coverage profiles (noted red and blue below):</p>
  <p><a href="https://ibb.co/6X34kfq" rel="nofollow noreferrer"></a></p>
  <p>I then thought that the low coverage sequencing profile around 4x might be a eukaryotic contaminant like a acarians, however when I blast the BUSCOs present on these low coverage scaffolds I get hits that are very close to the genome of my species...</p>
  <p>Does anyone have any idea what these are?</p>
  <p>here is an output of the <code>contigsTable.csv</code> where the two first row are scaffold with low coverage in the figure, and two last are scaffold with high coverage in the figure</p>
  <p><a href="https://i.stack.imgur.com/Dm85F.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/Dm85F.png" alt="enter image description here" /></a></p>
  <p>FRC output</p>
  <p><a href="https://i.stack.imgur.com/Z9pTV.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/Z9pTV.png" alt="enter image description here" /></a></p>
  <p>Coverage distribution</p>
  <p><a href="https://i.stack.imgur.com/jDU6S.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/jDU6S.png" alt="enter image description here" /></a></p>
  <p>Here is an Icarus summary of the assembly :</p>
  <pre><code>Assembly
  # contigs (&gt;= 0 bp) 1038631
  # contigs (&gt;= 1000 bp) 120132
  # contigs (&gt;= 5000 bp) 22245
  # contigs (&gt;= 10000 bp) 9986
  # contigs (&gt;= 25000 bp) 1322
  # contigs (&gt;= 50000 bp) 97
  Total length (&gt;= 0 bp) 655530043
  Total length (&gt;= 1000 bp) 451497861
  Total length (&gt;= 5000 bp) 260894112
  Total length (&gt;= 10000 bp) 174183054
  Total length (&gt;= 25000 bp) 45006012
  Total length (&gt;= 50000 bp) 5956145
  # contigs 214542
  Largest contig 120620
  Total length 519138286
  GC (%) 32.94
  N50 5062
  N75 1624
  L50 21982
  L75 71030
  # N's per 100 kbp 22.28
  </code></pre>
  <p>Here is the BUSCO summary as well :</p>
  <pre><code>2544 Complete BUSCOs (C)
  2312 Complete and single-copy BUSCOs (S)
  232 Complete and duplicated BUSCOs (D)
  1060 Fragmented BUSCOs (F)
  811 Missing BUSCOs (M)
  4415 Total BUSCO groups searched
  C:57.7%[S:52.4%,D:5.3%],F:24.0%,M:18.3%,n:4415
  </code></pre>
  <p>EDIT</p>
  <p>I ran the fastq sequences with another aligner (MEGAHIT) to see if it was not because of an assembly issue and I got the same profils coverage see here :</p>
  <p><a href="https://i.stack.imgur.com/6cq6m.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/6cq6m.png" alt="enter image description here" /></a></p>
   9693: <p>This could be organism-specific. We don't have a lot of info so far, so I would check a few more things:</p>
  <p>Run something like <a href="https://github.com/vezzi/FRC_align" rel="nofollow noreferrer">FRC_align</a>. Check if there's a clear signal between regions flagged as suspicious by it and your coverage graph.</p>
  <p>Is it a eukaryote? Plant? Check where mitchondria and chloroplasts are on the plot. They will have different GC/coverage signals than the rest of your assembly, which is fine, expected even.</p>
  <p>Worried about contamination? Run <a href="https://ccb.jhu.edu/software/kraken2/" rel="nofollow noreferrer">kraken2</a> on your raw data and see what you get there.</p>
  <p>Run <a href="http://www.repeatmasker.org/" rel="nofollow noreferrer">RepeatMasker</a> and check if repetive regions contribute to the effect you see.</p>
  <p>Finally, unless your specimen is low heterozygosity, haploid, or inbred, you probably have some effect from ploidy. There are numerous ways to check that. A self-self dot plot with <a href="http://mummer.sourceforge.net/" rel="nofollow noreferrer">MUMmer</a> and looking coverage histograms are a good start. The idea is that you should see two peaks (let's assume diploid). One for the split haplotigs, and one for collapsed.</p>
  <p>I checked the GC distribution of 45 genomes in your order. It's kind of all over the place, but there are some bimodal ones:
  <a href="https://i.stack.imgur.com/APLhU.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/APLhU.png" alt="GC distributions" /></a></p>
  <p>What does GC vs Length look like? Here's the one from the 45 genomes mentioned above:
  <a href="https://i.stack.imgur.com/Yme7I.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/Yme7I.png" alt="GC vs Length" /></a></p>
  