iSeq: An integrated tool to fetch public sequencing data

Abstract

AbstractHigh-throughput sequencing technologies (Next Generation Sequencing; NGS) are increasingly utilized by researchers to tackle a diverse array of biological inquiries. Leveraging the remarkable scale and efficiency of modern sequencing, significant advancements are made across various fields, spanning from genome analysis to the intricate dynamics of protein-nucleic acid interactions. Recognizing that NGS data harbors rich biological information, the International Nucleotide Sequence Database Collaboration (INSDC) was established nearly 40 years ago to collect and disseminate public nucleotide sequence data and associated metadata. The National Genomics Data Center (NGDC) has also provided open access to vast amounts of raw sequence data. These databases have greatly enhanced the capacity for reanalyzing NGS data. In recent years, amid the rise of large language models, biological sequences and data have emerged as inputs for training models to address biological challenges. However, methods for programmatically accessing this public sequencing data remain limited. To address this gap, we have developed iSeq, an integrated tool that allows for quick and straightforward retrieval of metadata and NGS data via the command-line interface. iSeq is currently the only tool that supports simultaneous retrieval from multiple databases (GSA, SRA, ENA, DDBJ, and GEO). Additionally, iSeq supports a wide range of accession formats as input and features parallel downloads, multi-threaded processes, and FASTQ file merging. It is freely available on Bioconda (https://anaconda.org/bioconda/iseq) and GitHub (https://github.com/BioOmics/iSeq).HighlightsiSeq supports multiple databases for accessing a wide range of raw sequencing data and metadata.iSeq supports at least 25 different accession formats as input.iSeq supports parallel downloads, multi-threaded processes, FASTQ file merging, and integrity verification.