Answers.Body: <p>You might want to look into <a href="https://github.com/rrwick/Unicycler" rel="noreferrer">Unicycler</a> (manuscript with more information <a href="http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005595" rel="noreferrer">can be found here</a>); even though it is supposed to be used with bacterial genomes only, it might work well with a small genome such as a mitochondrion's.</p>
  
  <p><a href="https://i.sstatic.net/wq02F.png" rel="noreferrer"><img src="https://i.sstatic.net/wq02F.png" alt="enter image description here"></a></p>
  
  <p>Beware that if you happen to have very long reads, you might end up with an assembly with multiple copies of the circular genome: you might want to look into <a href="https://github.com/sanger-pathogens/circlator" rel="noreferrer">circlator</a> then.</p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-07-26T11:36:21.933Z
Answers.Text: Mitochondria **are** bacteria. Their long co-evolution as endosymbiotes may have had an influence in some of their genomic characteristics, though.
Answers.UserDisplayName: bli
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-07-26T12:44:35.080Z
Answers.Text: Exactly; in fact, I'm not aware of any bacteria with a ~32kb genome :)
Answers.UserDisplayName: mgalardini
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-07-31T23:23:13.073Z
Answers.Text: This worked well for me. I got a single 21 kb circular contig with all the expected mt genes. Thanks for alerting me to this software!
Answers.UserDisplayName: Tom Harrop
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-07-26T10:25:29.833Z
Answers.LastActivityDate: 2017-07-26T10:30:40.230Z
Answers.LastEditDate: 2017-07-26T10:30:40.230Z
Answers.UserDisplayName: mgalardini
Body: <p>Low coverage MinION reads should be useful to close gaps and resolve repeats left by short-read assemblers. However, I haven't had any success with the software I know about. I'm aware of the following packages, either for scaffolding or closing gaps in short-read assemblies using long reads:</p>
  
  <ul>
  <li><a href="https://github.com/warrenlr/LINKS/" rel="noreferrer"><code>LINKS</code></a></li>
  <li><a href="https://sourceforge.net/projects/operasf" rel="noreferrer"><code>OPERA-LG</code></a></li>
  <li><a href="https://github.com/mdcao/npScarf" rel="noreferrer"><code>npScarf</code></a></li>
  <li><a href="https://sourceforge.net/projects/pb-jelly" rel="noreferrer"><code>PBJelly</code></a></li>
  <li><a href="https://www.baseclear.com/genomics/bioinformatics/basetools/SSPACE-longread" rel="noreferrer"><code>SSPACE-longread</code></a></li>
  </ul>
  
  <p>I've tried <code>npScarf</code> and <code>LINKS</code>, and they ran successfully but didn't resolve the gaps in my assembly. I couldn't get <code>PBJelly</code> and <code>OPERA-LG</code> to run with the current versions of <code>BLASR</code> and <code>samtools</code>, and both packages seem not to be maintained. I have not tried <code>SSPACE-longread</code> because it's not open source.</p>
  
  <p><strong>What software can I use to fill gaps and resolve repeats in a short-read assembly with low-coverage Nanopore data?</strong></p>
  
  <hr>
  
  <h3>More information</h3>
  
  <p>I'm finishing a mitochondrial genome. I have a 17 kb short read assembly with one gap. This was made from 2x150b paired-end reads from a TruSeq PCR-free library with a 400 b insert size. Molecular data suggests the genome may be around 32 kb.</p>
  
  <p>After mapping short reads against the short read assembly, <code>Pilon</code> identified a tandem repeat of 156 bp in an AT-rich region, but wasn't able to close the gap.</p>
  
  <p>I have 1.4 Gb of MinION rapid reads with an L50 of 8808 b. I mapped these reads against the short read assembly, and I can see reads that span the gap. I seem to have the information required to close the gap, but I don't know how to do it.</p>
  
  <p>The organism has a nuclear genome > 600 Mb, so long read coverage is low. Despite this, I tried a <em>de novo</em> <code>Canu</code> assembly of the Nanopore reads, and I pulled out a 39 kb contig containing mitochondrial genes. Most genes on this contig are duplicated and fragmented, and <code>Pilon</code> wasn't able to improve it. </p>
  
  <p>Thanks for reading!</p>
  
Tags: <nanopore><long-reads><repeat-elements><scaffold>
Title: How can I use Nanopore reads to close gaps or resolve repeats in a short-read assembly?
ThreadText: # How can I use Nanopore reads to close gaps or resolve repeats in a short-read assembly?
  
  (Asked by: username_0 on 2017-07-26)
  
  Low coverage MinION reads should be useful to close gaps and resolve repeats left by short-read assemblers. However, I haven't had any success with the software I know about. I'm aware of the following packages, either for scaffolding or closing gaps in short-read assemblies using long reads:
  
  * [`LINKS`](https://github.com/warrenlr/LINKS/)
  * [`OPERA-LG`](https://sourceforge.net/projects/operasf)
  * [`npScarf`](https://github.com/mdcao/npScarf)
  * [`PBJelly`](https://sourceforge.net/projects/pb-jelly)
  * [`SSPACE-longread`](https://www.baseclear.com/genomics/bioinformatics/basetools/SSPACE-longread)
  
  I've tried `npScarf` and `LINKS`, and they ran successfully but didn't resolve the gaps in my assembly. I couldn't get `PBJelly` and `OPERA-LG` to run with the current versions of `BLASR` and `samtools`, and both packages seem not to be maintained. I have not tried `SSPACE-longread` because it's not open source.
  
  **What software can I use to fill gaps and resolve repeats in a short-read assembly with low-coverage Nanopore data?**
  
  ---
  
  ### More information
  
  I'm finishing a mitochondrial genome. I have a 17 kb short read assembly with one gap. This was made from 2x150b paired-end reads from a TruSeq PCR-free library with a 400 b insert size. Molecular data suggests the genome may be around 32 kb.
  
  After mapping short reads against the short read assembly, `Pilon` identified a tandem repeat of 156 bp in an AT-rich region, but wasn't able to close the gap.
  
  I have 1.4 Gb of MinION rapid reads with an L50 of 8808 b. I mapped these reads against the short read assembly, and I can see reads that span the gap. I seem to have the information required to close the gap, but I don't know how to do it.
  
  The organism has a nuclear genome > 600 Mb, so long read coverage is low. Despite this, I tried a *de novo* `Canu` assembly of the Nanopore reads, and I pulled out a 39 kb contig containing mitochondrial genes. Most genes on this contig are duplicated and fragmented, and `Pilon` wasn't able to improve it.
  
  Thanks for reading!
  
  **Tags:** nanopore, long-reads, repeat-elements, scaffold
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2017-07-26. Score: 6 | Accepted answer
  
  You might want to look into [Unicycler](https://github.com/rrwick/Unicycler) (manuscript with more information [can be found here](http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005595)); even though it is supposed to be used with bacterial genomes only, it might work well with a small genome such as a mitochondrion's.
  
  [![enter image description here](https://i.sstatic.net/wq02F.png)](https://i.sstatic.net/wq02F.png)
  
  Beware that if you happen to have very long reads, you might end up with an assembly with multiple copies of the circular genome: you might want to look into [circlator](https://github.com/sanger-pathogens/circlator) then.
  
  > **Comments:**
  > **username_2**: Mitochondria **are** bacteria. Their long co-evolution as endosymbiotes may have had an influence in some of their genomic characteristics, though.  
  > **username_1**: Exactly; in fact, I'm not aware of any bacteria with a ~32kb genome :)  
  > **username_0**: This worked well for me. I got a single 21 kb circular contig with all the expected mt genes. Thanks for alerting me to this software!  
  
  ---
  
  