Creating SQL of Raw Reads with Metadata/Environmental Data?
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2.3 years ago
anabaena • 0

Essentially I have a a large amount of read sets from across the world and along with those read sets I have a .csv of the corresponding environmental data (Location, O2, etc.). The goal is to go through and run assemblies with that data, but I need the assembly outputs to be matched with the meta data of the raw read samples, so I can study the bio geography for strains of interest. So is anyone aware of a pipeline in which I can organize this information in a database (i.e. reads with assemblies corresponding to location, etc.)? Or is creating a SQL database the best option? I am also looking into Anvi'o and I know you can create a contigs db from assembled contigs but I haven't read anything else. Advice would be appreciated, thank you all.

SQL Metagenomics metadata Anvio • 364 views
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