1
$\begingroup$

Similar to this unanswered question on Biostars, 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 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.

Improve this question
$\endgroup$
2
  • 1
    $\begingroup$ @M__ Added the quotation and clarified that I am doing fungal genome assembly $\endgroup$ Commented Aug 28, 2023 at 15:03
  • $\begingroup$ 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. $\endgroup$ Commented Aug 28, 2023 at 15:14

0

Reset to default

Start asking to get answers

Find the answer to your question by asking.

Ask question

Explore related questions

See similar questions with these tags.