Uploading own files

For each project, MGX provides dedicated storage (2.30) in order to allow users to provide custom data, subsequently to be used with analysis pipelines. Thus, own sequence collections or HMM model files for genes of interest can easily be uploaded and later on be included into analysis pipelines.

Figure 2.30: Each project includes flat storage where custom data can be stored, e.g. own FASTA files to be used as reference databases for metagenome analysis.
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While it may be necessary to implement an own pipeline depending on the desired kind of analysis, the MGX repository hosts predefined pipeline templates addressing the most common cases: The “BestHit-Blast” template can be used to annotate metagenome sequences with the description of a Blast hit after the user has uploaded a FASTA file containing amino acid sequences, and the “BestHit-HMM” template provides the same functionality for hidden Markov models (HMMs).

Sebastian Jaenicke, 2020-04-28