Obtaining Data

2. Obtaining Data#

You can either bring your own FASTQ files or download public datasets.

2.1. Public Repositories#

  • NCBI SRA

  • ENA (European Nucleotide Archive)

  • MG-RAST (for some community projects)

2.2. Example (SRA tools)#

prefetch SRRXXXXXXX
fasterq-dump SRRXXXXXXX -O fastq/ --split-files --threads 8

2.3. Metadata#

Always prepare a metadata.tsv with at least:

  • SampleID

  • Condition

  • Replicate

  • Batch

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