Body: <p>Similar to <a href="https://www.biostars.org/p/379046/" rel="nofollow noreferrer">this unanswered question on Biostars</a>, I am using MaSuRCA for the first time and want to know how other MaSuRCA users are determining fragment mean and fragment stdev. My understanding is that FastQC measures read length, which differs from fragment length.</p>
  <p><a href="https://diposit.ub.edu/dspace/bitstream/2445/195686/1/727000.pdf" rel="nofollow noreferrer">This paper</a> that used MaSuRCA for a bird genome assembly mentions the parameters they used but not how those parameters were determined: &quot;MaSuRCA was run applying the following parameters: fragment mean (422), fragment stdev (312), and estimated genome size (1.2 Gbp).&quot;</p>
  <p>I am using Illumina, Nanopore, and PacBio reads for fungal genome assembly. Any advice on which tool(s) to use to determine fragment mean and stdev for MaSuRCA would be appreciated.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-08-28T15:03:24.407Z
Comments.Text: @M__ Added the quotation and clarified that I am doing fungal genome assembly
Comments.UserDisplayName: juliadouglasf
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-08-28T15:14:08.967Z
Comments.Text: Thanks for the edits and added information @juliadouglasf .. difficult genome BTW (Mycorrhizae I assume), but definitely an interesting and worth while area and good luck with the question.
Comments.UserDisplayName: M__
Tags: <assembly><reads>
Title: Determining fragment mean and fragment stdev for MaSuRCA config file
ThreadText: # Determining fragment mean and fragment stdev for MaSuRCA config file
  
  (Asked by: username_0 on 2023-08-28)
  
  Similar to [this unanswered question on Biostars](https://www.biostars.org/p/379046/), I am using MaSuRCA for the first time and want to know how other MaSuRCA users are determining fragment mean and fragment stdev. My understanding is that FastQC measures read length, which differs from fragment length.
  
  [This paper](https://diposit.ub.edu/dspace/bitstream/2445/195686/1/727000.pdf) that used MaSuRCA for a bird genome assembly mentions the parameters they used but not how those parameters were determined: "MaSuRCA was run applying the following parameters: fragment mean (422), fragment stdev (312), and estimated genome size (1.2 Gbp)."
  
  I am using Illumina, Nanopore, and PacBio reads for fungal genome assembly. Any advice on which tool(s) to use to determine fragment mean and stdev for MaSuRCA would be appreciated.
  
  **Tags:** assembly, reads
  
  > **Comments:**
  > **username_0**: @username_1 Added the quotation and clarified that I am doing fungal genome assembly  
  > **username_1**: Thanks for the edits and added information @username_0 .. difficult genome BTW (Mycorrhizae I assume), but definitely an interesting and worth while area and good luck with the question.  
  
  ---
  
  ## 0 answers
  
  