Are there recommended pipelines/methods for dereplicating LARGE custom databases? #43
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I was hoping to find the process for dereplicating the provided sylph databases (e.g. from the GTDB). In lieu of that, are there any recommended pipelines/methods for dereplicating large custom databases? I'm not a bioinformatician, but I can't make use of the segmented genomes after profiling with gtdb-r220-c200-dbv1.syldb. |
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@bryantmurphy The GTDB-R220 database is the species-level dereplicated genomes from GTDB. They have a specific pipeline for dereplication, see https://academic.oup.com/nar/article/50/D1/D785/6370255 For dereplicating large custom databases, see https://github.com/MrOlm/drep (quite popular) or https://github.com/raufs/skDER for possible tools. |
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Yes, this is exactly how gtdb-r220-c200... was made. See https://sylph-docs.github.io/taxonomic-profiling-tutorial/: Step 1. for how the provided sylph database was created. |
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@bryantmurphy The GTDB-R220 database is the species-level dereplicated genomes from GTDB. They have a specific pipeline for dereplication, see https://academic.oup.com/nar/article/50/D1/D785/6370255
For dereplicating large custom databases, see https://github.com/MrOlm/drep (quite popular) or https://github.com/raufs/skDER for possible tools.