Assessing and assuring interoperability of a genomics file format.

ABSTRACT:

Motivation

Bioinformatics software tools operate largely through the use of specialized genomics file formats. Often these formats lack formal specification, making it difficult or impossible for the creators of these tools to robustly test them for correct handling of input and output. This causes problems in interoperability between different tools that, at best, wastes time and frustrates users. At worst, interoperability issues could lead to undetected errors in scientific results.

Results

We developed a new verification system, Acidbio, which tests for correct behavior in bioinformatics software packages. We crafted tests to unify correct behavior when tools encounter various edge cases-potentially unexpected inputs that exemplify the limits of the format. To analyze th

SUBMITTER: Niu YN 

PROVIDER: S-EPMC9237710 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature