Answers.Body: <p>To add the &quot;do not assemble your genome&quot; answers. There might be specific circumstances when you would actually like to do that. For example, if the 30x you got are HiFi long reads and have a reason to suspect there are some interesting large rearrangements in your genome (rare disease?), it might be informative to actually assemble the genome and compare it to the reference to find these rearrangements.</p>
  <p>Of course there is also plenty of possibilities in between (still assuming long reads), for example to map your sequencing data to a pan-genome graph or simply use a mapper that is aware of genomic rearrangements (like <a href="https://github.com/philres/ngmlr" rel="nofollow noreferrer">ngmlr</a>) and call the <a href="https://www.nature.com/articles/s41592-018-0001-7" rel="nofollow noreferrer">structural variants</a>.</p>
  <p>But in the end it boils down to two aspects you did not mention in your question: What would you like to learn about your genome?</p>
  
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Answers.CreationDate: 2022-09-28T14:34:10.237Z
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Answers.UserDisplayName: Kamil S Jaron
Answers.Body: <p>Given you've tagged this as 'human-genome' there is likely little value in performing genome assembly. De-novo assembly of WGS is generally for non-model organisms without a reference genome available, and would require much higher than 30X coverage (and ideally long reads). By providing the BAM and VCF, they'e already saved you some upstream work unless there are needs to re-process the data from FASTQ</p>
  
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Answers.UserDisplayName: Chris_Rands
Answers.Body: <p>No, assembling won't tell you anything new. When working with organisms whose reference genome is known, all you care about is where <em>your</em> sequences differ from the reference. If you know where your sequences differ, then you can infer the rest, they will be whatever is in the reference.</p>
  <p>All you want to do is identify <em>variants</em>, those sites where your genome differs from the reference. That's what the VCF file contains. Bear in mind that the reference isn't some sort of platonic ideal of the perfect human, it's just the collected, pooled DNA of <a href="https://en.wikipedia.org/wiki/Reference_genome#Human_reference_genome" rel="nofollow noreferrer">13 anonymous, apparently healthy individuals</a>. You can expect anywhere from about 3 to 5 million differences in your own genome, the overwhelming majority of which will be completely innocuous.</p>
  <p>Since you already have your VCF file, your list of variants, that's all you need to investigate. If you really want to, you can make your assembly by taking the reference genome and then adding the variants in your VCF file, but it won't be of much practical use.</p>
  
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Answers.UserDisplayName: terdon
Body: <p>I've had my whole genome sequenced (at 30x average coverage) by a lab, and they have provided the raw files to me (BAM, FASTQ, and VCF).</p>
  <p>How can I assemble it?</p>
  <p>And does assembly provide any further insights that I can't get from the separated fragments?</p>
  <p>I'd like to assemble and annotate it, and find insights, but I don't know where to start.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-09-24T19:46:45.707Z
Comments.Text: What do you want to achieve by 'assembling' it?  That's usually restricted to random organisms where we don't have a reference sequence. Your VCF/BAM/FASTQ data has already been mapped to an assembled genome so it doesn't really make sense to do an assembly of it. You could certainly annotate it thought, but thats a different question altogether.
Comments.UserDisplayName: user438383
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Comments.Text: It would be useful to know the reference genome.
Comments.UserDisplayName: M__
Tags: <assembly><human-genome><sequence-annotation>
Title: How can I assemble my genome from raw files?
ThreadText: # How can I assemble my genome from raw files?
  
  (Asked by: username_0 on 2022-09-24)
  
  I've had my whole genome sequenced (at 30x average coverage) by a lab, and they have provided the raw files to me (BAM, FASTQ, and VCF).
  
  How can I assemble it?
  
  And does assembly provide any further insights that I can't get from the separated fragments?
  
  I'd like to assemble and annotate it, and find insights, but I don't know where to start.
  
  **Tags:** assembly, human-genome, sequence-annotation
  
  > **Comments:**
  > **username_1**: What do you want to achieve by 'assembling' it?  That's usually restricted to random organisms where we don't have a reference sequence. Your VCF/BAM/FASTQ data has already been mapped to an assembled genome so it doesn't really make sense to do an assembly of it. You could certainly annotate it thought, but thats a different question altogether.  
  > **username_2**: It would be useful to know the reference genome.  
  
  ---
  
  ## 3 answers
  
  ### Answer by username_3 on 2022-09-28. Score: 2
  
  To add the "do not assemble your genome" answers. There might be specific circumstances when you would actually like to do that. For example, if the 30x you got are HiFi long reads and have a reason to suspect there are some interesting large rearrangements in your genome (rare disease?), it might be informative to actually assemble the genome and compare it to the reference to find these rearrangements.
  
  Of course there is also plenty of possibilities in between (still assuming long reads), for example to map your sequencing data to a pan-genome graph or simply use a mapper that is aware of genomic rearrangements (like [ngmlr](https://github.com/philres/ngmlr)) and call the [structural variants](https://www.nature.com/articles/s41592-018-0001-7).
  
  But in the end it boils down to two aspects you did not mention in your question: What would you like to learn about your genome?
  
  
  ---
  
  ### Answer by username_4 on 2022-09-24. Score: 2
  
  Given you've tagged this as 'human-genome' there is likely little value in performing genome assembly. De-novo assembly of WGS is generally for non-model organisms without a reference genome available, and would require much higher than 30X coverage (and ideally long reads). By providing the BAM and VCF, they'e already saved you some upstream work unless there are needs to re-process the data from FASTQ
  
  
  ---
  
  ### Answer by username_5 on 2022-09-25. Score: 2
  
  No, assembling won't tell you anything new. When working with organisms whose reference genome is known, all you care about is where *your* sequences differ from the reference. If you know where your sequences differ, then you can infer the rest, they will be whatever is in the reference.
  
  All you want to do is identify *variants*, those sites where your genome differs from the reference. That's what the VCF file contains. Bear in mind that the reference isn't some sort of platonic ideal of the perfect human, it's just the collected, pooled DNA of [13 anonymous, apparently healthy individuals](https://en.wikipedia.org/wiki/Reference_genome#Human_reference_genome). You can expect anywhere from about 3 to 5 million differences in your own genome, the overwhelming majority of which will be completely innocuous.
  
  Since you already have your VCF file, your list of variants, that's all you need to investigate. If you really want to, you can make your assembly by taking the reference genome and then adding the variants in your VCF file, but it won't be of much practical use.
  
  
  ---
  
  