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.
