Importing links to data stored at SRA, ENA, Amazon S3 and BaseSpace

In this tutorial the steps to import links to following online repositories are described:

  • NCBI (SRA): link to data from the Sequence Read Archive (SRA) repository, based on the NCBI run accession number.
  • EMBL-EBI (ENA): link to data from the ENA repository, based on the EMBL-EBI run accession number.
  • Amazon (S3): link to data uploaded to a client-specific data bucket hosted at the Amazon S3 storage repository.
  • BaseSpace: link to data uploaded to a data folder hosted on Illumina BaseSpace.

Sequence read sets

A sequence read set is designed to hold large sets of short reads generated by next generation sequencing (NGS). Base sequences and their associated quality scores are stored for single-end and paired-end reads, originating from various high-throughput sequencing platforms such as Illumina, Ion Torrent, PacBio, Oxford Nanopore, etc.

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