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Uploading raw Nanopore data to ENA using ENAdumper

Prerequisites

  1. Register a Webin account at ENA for submitting files
  2. Register a study at ENA and get a study ID
  3. Register your samples to acquire the sample sheet from ENA
  4. The sample sheet will act as a key-file linking the sample names to the corresponding ENA sample IDs. Example below:
TYPE ACCESSION ALIAS
SAMPLE ERS00000001 S1
SAMPLE ERS00000002 S2
SAMPLE ERS00000003 S3
SAMPLE ERS00000004 S4
SAMPLE ERS00000005 S5
SAMPLE ERS00000006 S6

Running the ENAdumper workflow

  1. Given the typical size of a usual Fast5 dataset, ENAdumper processes and uploads one sample at a time
  2. The main input is a path to a directory containing Fast5 files that the user wants to upload
  3. Example command for uploading Fast5 data with ENAdumper:
    ENAdumper --fast5_dir /path/to/fast5 --key sample_sheet.tsv --sample S1 --study PRJEB00001 -user Webin-0001 -pass Banana1
  4. ENAdumper will split and compress the Fast5 files into multiple batches, which can be set using the --processes option
  5. After upload is complete, a template spreadsheet will be generated that can be submitted to include the files in the permanent archive
  6. It is highly recommended to double-check the template spreadsheet before submitting it to ENA