After doing illumina sequencing, I have found forward (121.5 gb) and reverse (121.5 gb) fastq files of Fasciola gigantica. I want to do assembly using galaxy. Is it possible for this large size data? If yes, please tell me the steps. Thank you
This is a good question! Yes, you can certainly give this a try at a public Galaxy server!
Data storage
The size of the raw data files by itself isn’t a bottleneck. Extra working space (aka scratch-space ) and BYOS (“bring your own storage”) varies by server. This is a good place to start to get oriented → How to access your Self Serve extended data storage at UseGalaxy servers!
Protocols
We have tutorials that demonstrate how to translate published methods into a Galaxy workflow. These can be good baselines then you can make adjustments to accommodate the characteristics of your target genome. Reviewing published protocols for your species or related species is usually important to learn about these factors since no assembly protocol is a “one size fits all”.
I would strongly recommended that you do some investigation into the read types others typically use and how they overcome the technical challenges involved with assembling this genome. This forum is not the best place to reach others who have done this with your particular species (but if they are here, please comment!). Instead, when working out “what” you want to do, a scientific forum will cast a wider net. Then, for the “how”, you can come back here if you can’t find the analogous tool or have problems using it. ![]()
Resources
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If you are new to Galaxy, getting oriented with the UI will help! This is my favorite quick guide. → Hands-on: Galaxy Basics for everyone / Galaxy Basics for everyone / Introduction to Galaxy Analyses
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Then, start here → Assembly / Tutorial List
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After assembly, you’ll want to explore what you have! You can proceed to here → Learning Pathway: Genome annotation for eukaryotes or here → Genome Annotation / Tutorial List
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And, while each tutorial includes a workflow, you can find the production quality workflows over at the IWC website here → https://iwc.galaxyproject.org/
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Then, public workflows can be reviewed at any public Galaxy server under the Histories → Public Workflows tab or you can try at the Community Hub here → GTN Pan-Galactic Workflow Search
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With production quality workflows at the
IWC Workflow Library https://iwc.galaxyproject.org/
I hope this gives you some options! ![]()