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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.

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  • $\begingroup$ Please edit the question to limit it to a specific problem with enough detail to identify an adequate answer. $\endgroup$
    – Community Bot
    Jun 10, 2022 at 13:06
  • $\begingroup$ Many tools prefer PB reads in their original BAM format. What kind of PB reads? HiFi? $\endgroup$
    – Maximilian Press
    Jun 12, 2022 at 19:07
  • $\begingroup$ Yes HiFi reads. I have the reads in fastq and fasta fromat. $\endgroup$
    – Amroon
    Jun 13, 2022 at 20:17

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Try hifiasm-meta (paper here). Whether it works depends on the abundance and the complexity. You may also try HiCanu.

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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
  2. Annotate your resulting long contigs (>500Kbp) using GTDB-tk
  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.
  7. Map your HiFi reads to the genome, see if you can close the remaining gap with e.g. SSpace-LongRead.

I'd suggest using this paper as an example for further workflow details.

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  • $\begingroup$ Thanks for your answer and the references $\endgroup$
    – Amroon
    Jun 22, 2022 at 8:09
  • $\begingroup$ @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: stackoverflow.com/help/someone-answers $\endgroup$
    – Maximilian Press
    Jun 22, 2022 at 16:39

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