blast2galaxy: a CLI and Python API for BLAST+ and DIAMOND searches on Galaxy servers

Abstract

Motivation: The Galaxy workflow system is an open-source platform supporting data-intensive research in life sciences, featuring a user-friendly web interface for complex analyses without extensive programming. It also offers a representational state transfer based API, enabling remote execution of specific tools. Galaxy supports similarity searches for nucleotide and amino acid sequences, with integrated tools like NCBI BLAST+ and DIAMOND. However, no specialized software currently exists for convenient use of NCBI BLAST+ and DIAMOND via the Galaxy API. Results: blast2galaxy is a Python package that uses the Galaxy API to run sequence alignments with NCBI BLAST+ and DIAMOND as Galaxy-wrapped tools on compatible servers. It includes a command-line interface that mirrors the CLI of BLAST+ and DIAMOND and a high-level Python API for direct alignments from Python applications. The package relies on bioblend for communication with the Galaxy API.