Abstract
BACKGROUND: The rapid increase in publicly available microbial and metagenomic data has created a growing demand for tools that can efficiently perform custom large-scale comparative searches and functional annotation. While BLAST + remains the standard for sequence similarity searches, population-level studies often require custom scripting and manual curation of results, which can present barriers for many researchers. RESULTS: We developed SeqForge, a scalable, modular command-line toolkit that streamlines alignment-based searches and motif mining across large genomic datasets. SeqForge automates BLAST + database creation and querying, integrates amino acid motif discovery, enables sequence and contig extraction, and curates results into structured, easily parsed formats. The platform supports diverse input formats, parallelized execution for high-performance computing environments, and built-in visualization tools. Benchmarking demonstrates that SeqForge achieves near-linear runtime scaling for computationally intensive modules while maintaining modest memory usage. CONCLUSIONS: SeqForge lowers the computational barrier for large-scale meta/genomic exploration, enabling researchers to perform population-scale BLAST searches, motif detection, and sequence curation without custom scripting. The toolkit is freely available and platform-independent, making it suitable for both personal workstations and high-performance computing environments.