Advice on using ddocent with wgs data

[Paige M.]

Hello All,

I have recently been using dDocent with a large radseq dataset.  I am currently running the revised RefMapOpt.sh script and am really impressed with the mapping results I am getting and the speed with which the software actually runs the analysis on my dataset (I did use a subset of my population for this as suggested - but wow  it is so much faster than Stacks2 was with the same task and I can understand the output much more clearly for evaluating the options).  The genome size for the organism I am using this for is ~1.8Gb

I am considering whether dDocent could be run on WGS data?  I tried searching this forum, but found little mention of whether this might be successful?  I already know Stacks2 doesn't work well with this type of data.  We have a completed analysis using BBTools and the output is only so-so, and I'd really like to complete a different analysis for comparison.  I think the main problem is that we have don't have a reference genome (this is not a model organism) and the draft one built by our provider is just not good enough.  The genome size for the organism is only ~400kb and I do have access to a good HPC cluster.

Has anyone used dDocent for a similar purpose with success? Or, failed? Or, have more experience in general with this type of stuff and feel like offering any advice?

Thank you!!!

[Jon Puritz]

Hi Paige,

It's not documented, but it is fully functional here (https://github.com/The-Eastern-Oyster-Genome-Project/2023_Eastern_Oyster_Haplotig_Masked_Genome/tree/main/scripts).  You'll need to make sure that Picard is installed and in your $PATH.  There is a markdown file in the repo showing how to use it.

Jon

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Jon Puritz, PhD

Assistant Professor
Department of Biological Sciences
University of Rhode Island
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