Answers.Body: <p>Try <a href="https://github.com/xfengnefx/hifiasm-meta" rel="nofollow noreferrer">hifiasm-meta</a> (<a href="https://www.nature.com/articles/s41592-022-01478-3" rel="nofollow noreferrer">paper here</a>). Whether it works depends on the abundance and the complexity. You may also try HiCanu.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-06-14T22:24:53.123Z
Answers.LastActivityDate: 2022-06-14T22:24:53.123Z
Answers.UserDisplayName: user172818
Answers.Body: <p>I would suggest the following workflow, understanding you to have metagenomic HiFi sequencing that you <strong>know</strong> to include your species of interest at high abundance:</p>
  <ol>
  <li>metagenomic assembly of HiFi with <a href="https://www.nature.com/articles/s41592-020-00971-x" rel="nofollow noreferrer">metaFlyE</a></li>
  <li>Annotate your resulting long contigs (&gt;500Kbp) using <a href="https://scholar.google.com/citations?view_op=view_citation&amp;hl=en&amp;user=A87iE7wAAAAJ&amp;citation_for_view=A87iE7wAAAAJ:Tiz5es2fbqcC" rel="nofollow noreferrer">GTDB-tk</a></li>
  <li>Look for your Anaeroplasma among long contigs</li>
  <li>Assess whether your genome is closed.</li>
  <li>If the genome is closed, you are done.</li>
  <li>If the genome is not closed, you need to close it. Assess its completeness using e.g. <a href="https://ecogenomics.github.io/CheckM/" rel="nofollow noreferrer">checkM</a>.</li>
  <li>Map your HiFi reads to the genome, see if you can close the remaining gap with e.g. <a href="https://www.pacb.com/publications/gapfinisher-a-reliable-gap-filling-pipeline-for-sspace-longread-scaffolder-output/" rel="nofollow noreferrer">SSpace-LongRead</a>.</li>
  </ol>
  <p>I'd suggest using <a href="https://www.nature.com/articles/s41587-021-01130-z" rel="nofollow noreferrer">this paper</a> as an example for further workflow details.</p>
  
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Answers.CreationDate: 2022-06-22T08:09:33.010Z
Answers.Text: Thanks for your answer and the references
Answers.UserDisplayName: Amroon
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Answers.CreationDate: 2022-06-22T16:39:12.950Z
Answers.Text: @Amroon, you are very welcome. By the way, it's traditional on SE sites to upvote answers that you find helpful (there are now a couple of reasonable answers to your question), and accept the answer that you see as helping you solve the problem. For more info on responding to answers on SE, see here: https://stackoverflow.com/help/someone-answers
Answers.UserDisplayName: Maximilian Press
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Answers.CreationDate: 2022-06-14T20:57:16.067Z
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Answers.UserDisplayName: Maximilian Press
Body: <p>I have a fasta file containing reads generated by PacBio HiFi whole genome sequencing of a feces sample from mouse.</p>
  <p>I would like to use this dataset to generate an assembled circularized genome for an Anaeroplasma organism known to be in this sample.</p>
  <p>I am familiar with Linux and R. I would very much appreciate your advice on the needed steps and the required tools or R packages.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-06-10T13:06:29.710Z
Comments.Text: Please edit the question to limit it to a specific problem with enough detail to identify an adequate answer.
Comments.UserDisplayName: Community
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-06-12T19:07:27.693Z
Comments.Text: Many tools prefer PB reads in their original BAM format. What kind of PB reads? HiFi?
Comments.UserDisplayName: Maximilian Press
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-06-13T20:17:10.983Z
Comments.Text: Yes HiFi reads. I have the reads in fastq and fasta fromat.
Comments.UserDisplayName: Amroon
Tags: <assembly><linux><wgs><pacbio>
Title: Assemble Anaeroplasma species genome from metagenomic PacBio data
ThreadText: # Assemble Anaeroplasma species genome from metagenomic PacBio data
  
  (Asked by: username_0 on 2022-06-10)
  
  I have a fasta file containing reads generated by PacBio HiFi whole genome sequencing of a feces sample from mouse.
  
  I would like to use this dataset to generate an assembled circularized genome for an Anaeroplasma organism known to be in this sample.
  
  I am familiar with Linux and R. I would very much appreciate your advice on the needed steps and the required tools or R packages.
  
  **Tags:** assembly, linux, wgs, pacbio
  
  > **Comments:**
  > **username_1**: Please edit the question to limit it to a specific problem with enough detail to identify an adequate answer.  
  > **username_2**: Many tools prefer PB reads in their original BAM format. What kind of PB reads? HiFi?  
  > **username_0**: Yes HiFi reads. I have the reads in fastq and fasta fromat.  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_3 on 2022-06-14. Score: 1
  
  Try [hifiasm-meta](https://github.com/xfengnefx/hifiasm-meta) ([paper here](https://www.nature.com/articles/s41592-022-01478-3)). Whether it works depends on the abundance and the complexity. You may also try HiCanu.
  
  
  ---
  
  ### Answer by username_2 on 2022-06-14. Score: 0
  
  I would suggest the following workflow, understanding you to have metagenomic HiFi sequencing that you **know** to include your species of interest at high abundance:
  
  1. metagenomic assembly of HiFi with [metaFlyE](https://www.nature.com/articles/s41592-020-00971-x)
  2. Annotate your resulting long contigs (>500Kbp) using [GTDB-tk](https://scholar.google.com/citations?view_op=view_citation&hl=en&user=A87iE7wAAAAJ&citation_for_view=A87iE7wAAAAJ:Tiz5es2fbqcC)
  3. Look for your Anaeroplasma among long contigs
  4. Assess whether your genome is closed.
  5. If the genome is closed, you are done.
  6. If the genome is not closed, you need to close it. Assess its completeness using e.g. [checkM](https://ecogenomics.github.io/CheckM/).
  7. Map your HiFi reads to the genome, see if you can close the remaining gap with e.g. [SSpace-LongRead](https://www.pacb.com/publications/gapfinisher-a-reliable-gap-filling-pipeline-for-sspace-longread-scaffolder-output/).
  
  I'd suggest using [this paper](https://www.nature.com/articles/s41587-021-01130-z) as an example for further workflow details.
  
  > **Comments:**
  > **username_0**: Thanks for your answer and the references  
  > **username_2**: @username_0, you are very welcome. By the way, it's traditional on SE sites to upvote answers that you find helpful (there are now a couple of reasonable answers to your question), and accept the answer that you see as helping you solve the problem. For more info on responding to answers on SE, see here: https://stackoverflow.com/help/someone-answers  
  
  ---
  
  