Answers.Body: <p>some additional information to your request.</p>
  <p><a href="https://ftp.ncbi.nlm.nih.gov/genomes/Viruses/FamilyPhylogeneticTree/Graph/SRR12707453.MN813694.1.gfa" rel="nofollow noreferrer">https://ftp.ncbi.nlm.nih.gov/genomes/Viruses/FamilyPhylogeneticTree/Graph/SRR12707453.MN813694.1.gfa</a></p>
  <p>it contain assembled by reference graph
  using ncbi tool saute(skesa) which will be public later.</p>
  <p>install bandage app and load this graph
  <a href="https://rrwick.github.io/Bandage/" rel="nofollow noreferrer">https://rrwick.github.io/Bandage/</a></p>
  <p>picture looks intriguing,I would say , run contain many errors located in one position.
  Reason? I don’t really know.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-11-04T21:14:31.980Z
Answers.Text: Yep... I don't know how circularization works. I guess it could be that binding the sequence generates every time some garbage in the union and so every RNA chain has a slightly different sequence at this point.
Answers.UserDisplayName: juanjo75es
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-11-02T23:25:07.397Z
Answers.LastActivityDate: 2020-11-02T23:25:07.397Z
Answers.UserDisplayName: user6690
Body: <p>I have applied two de novo genome assembly tools to data from the run SRR12707453, corresponding to a phage (I downloaded the data and have no relation with the authors of the study).</p>
  <p>Using rnaSPAdes I get many long contigs (&gt;50.000 bp). When analyzing the contigs using Quast against a reference genome (MN813694.1) most long contigs are discarded and the seventh-longest one is the only one selected. If I blast the other contigs I find correspondence with other phages, which makes me conclude that many phages were present in the same probe.</p>
  <p>This seventh contig has 47686 bp length, while the reference has 47713 bp length. But they are not equivalently arranged. Apparently, the genome was <a href="https://viralzone.expasy.org/3968?outline=all_by_species" rel="nofollow noreferrer">circularized</a> and then it was broken around the position 32400 in the reference. Also, the sequence does not match between positions 45000 and 45951 (in the reference), and a little misassembly seems to occur around position 46300.</p>
  <p>See here some screen captures for the Icarus visualization obtained with Quast:</p>
  <p><a href="https://i.sstatic.net/F56BQ.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/F56BQ.png" alt="enter image description here" /></a>
  <a href="https://i.sstatic.net/N4bFY.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/N4bFY.png" alt="enter image description here" /></a></p>
  <p>In contrast, using Quast with the contigs obtained from the other assembly tool, I get some differences. There is also a contig with almost the same size as the reference genome (47573 bp) that has exactly the same structure than the contig obtained with rnaSPAdes: circularized, broken around position 32400, does not match between position 45000 and 45951, and small misassemblie aronund position 46300. But there are also some contigs in which there is no break around position 32400.</p>
  <p><a href="https://i.sstatic.net/P2SSl.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/P2SSl.png" alt="enter image description here" /></a></p>
  <p>May I interpret that these contigs indicate that the phage genome is sometimes circularized and sometimes broken at position ~32400 and that's why some contigs don't find a sequence break at that position?</p>
  <p>Am I interpreting anything wrong? Any other conclusion can be obtained from the data?</p>
  <p>You can (temporaly) <a href="https://www.contignant.com/data/quast_results.zip" rel="nofollow noreferrer">download here the Quast results</a>.</p>
  
Tags: <sequence-analysis><assembly><reference-genome>
Title: Interpreting contig alignments to a reference genome
ThreadText: # Interpreting contig alignments to a reference genome
  
  (Asked by: username_0 on 2020-11-02)
  
  I have applied two de novo genome assembly tools to data from the run SRR12707453, corresponding to a phage (I downloaded the data and have no relation with the authors of the study).
  
  Using rnaSPAdes I get many long contigs (>50.000 bp). When analyzing the contigs using Quast against a reference genome (MN813694.1) most long contigs are discarded and the seventh-longest one is the only one selected. If I blast the other contigs I find correspondence with other phages, which makes me conclude that many phages were present in the same probe.
  
  This seventh contig has 47686 bp length, while the reference has 47713 bp length. But they are not equivalently arranged. Apparently, the genome was [circularized](https://viralzone.expasy.org/3968?outline=all_by_species) and then it was broken around the position 32400 in the reference. Also, the sequence does not match between positions 45000 and 45951 (in the reference), and a little misassembly seems to occur around position 46300.
  
  See here some screen captures for the Icarus visualization obtained with Quast:
  
  [![enter image description here](https://i.sstatic.net/F56BQ.png)](https://i.sstatic.net/F56BQ.png)
  [![enter image description here](https://i.sstatic.net/N4bFY.png)](https://i.sstatic.net/N4bFY.png)
  
  In contrast, using Quast with the contigs obtained from the other assembly tool, I get some differences. There is also a contig with almost the same size as the reference genome (47573 bp) that has exactly the same structure than the contig obtained with rnaSPAdes: circularized, broken around position 32400, does not match between position 45000 and 45951, and small misassemblie aronund position 46300. But there are also some contigs in which there is no break around position 32400.
  
  [![enter image description here](https://i.sstatic.net/P2SSl.png)](https://i.sstatic.net/P2SSl.png)
  
  May I interpret that these contigs indicate that the phage genome is sometimes circularized and sometimes broken at position ~32400 and that's why some contigs don't find a sequence break at that position?
  
  Am I interpreting anything wrong? Any other conclusion can be obtained from the data?
  
  You can (temporaly) [download here the Quast results](https://www.contignant.com/data/quast_results.zip).
  
  **Tags:** sequence-analysis, assembly, reference-genome
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2020-11-02. Score: 1
  
  some additional information to your request.
  
  <https://ftp.ncbi.nlm.nih.gov/genomes/Viruses/FamilyPhylogeneticTree/Graph/SRR12707453.MN813694.1.gfa>
  
  it contain assembled by reference graph
  using ncbi tool saute(skesa) which will be public later.
  
  install bandage app and load this graph
  <https://rrwick.github.io/Bandage/>
  
  picture looks intriguing,I would say , run contain many errors located in one position.
  Reason? I don’t really know.
  
  > **Comments:**
  > **username_0**: Yep... I don't know how circularization works. I guess it could be that binding the sequence generates every time some garbage in the union and so every RNA chain has a slightly different sequence at this point.  
  
  ---
  
  