ARA: a flexible pipeline for automated exploration of NCBI SRA datasets.

ABSTRACT:

Background

One of the most effective and useful methods to explore the content of biological databases is searching with nucleotide or protein sequences as a query. However, especially in the case of nucleic acids, due to the large volume of data generated by the next-generation sequencing (NGS) technologies, this approach is often not available. The hierarchical organization of the NGS records is primarily designed for browsing or text-based searches of the information provided in metadata-related keywords, limiting the efficiency of database exploration.

Findings

We developed an automated pipeline that incorporates the well-established NGS data-processing tools and procedures to allow easy and effective sampling of the NCBI SRA database records. Given a file with query nuc

SUBMITTER: Maurya A 

PROVIDER: S-EPMC10433097 | biostudies-literature | 2022 Dec

REPOSITORIES: biostudies-literature