Pysradb provides a convenient method to retrieve information from NCBI’s SRA database. Currently, pysradb is transitioning to phase out its dependency on an SRAmetadb.Sqlite file from the SRAdb project. While this file provides a fast, offline method of retrieving metadata found in SRA, it is very large; downloading the file represents a significant hurdle for users.

This project seeks to implement a search module for pysradb. This search module should be able to take in the user’s search query, parse it accordingly, query the SRA database and then retrieve and display the search results to the user. As the main consideration of this search module is user-friendliness, I propose several additional features to make pysradb more effective in achieving user's needs. These features include:

  • Accepting additional input parameters to finetune search results.
  • Processing and organisation of search results into more user-friendly formats.
  • Automatic generation of statistics and graphs, which serves to provide summary information about a search query for the user.

Student

Boshen Yan

Mentors

  • Amal Thomas
  • Marius van den Beek
  • Saket
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2020