# HTSinfer: inferring metadata from bulk Illumina RNA-Seq libraries

## TL;DR

HTSinfer is a tool that automatically infers metadata from RNA-Seq data, improving data reuse and reducing manual errors.

## Contribution

Introduces HTSinfer, a new open-source tool for inferring RNA-Seq metadata directly from sequencing data.

## Key findings

- HTSinfer accurately infers library source, type, and read orientation from RNA-Seq data.
- The tool uses genome sequences and diagnostic genes to determine metadata.
- HTSinfer is modular and encourages community contributions for future enhancements.

## Abstract

The Sequencing Read Archive is one of the largest and fastest-growing repositories of sequencing data, containing tens of petabytes of sequenced reads. Its data is used by a wide scientific community, often beyond the primary study that generated them. Such analyses rely on accurate metadata concerning the type of experiment and library, as well as the organism from which the sequenced reads were derived. These metadata are typically entered manually by contributors in an error-prone process, and are frequently incomplete. In addition, easy-to-use computational tools that verify the consistency and completeness of metadata describing the libraries to facilitate data reuse, are largely unavailable. Here, we introduce HTSinfer, a Python-based tool to infer metadata directly and solely from bulk RNA-sequencing data generated on Illumina platforms. HTSinfer leverages genome sequence information and diagnostic genes to rapidly and accurately infer the library source and library type, as well as the relative read orientation, 3′ adapter sequence and read length statistics. HTSinfer is written in a modular manner, published under a permissible free and open-source license and encourages contributions by the community, enabling easy addition of new functionalities, e.g. for the inference of additional metrics, or the support of different experiment types or sequencing platforms.

HTSinfer is released under the Apache License 2.0. Latest code is available via GitHub at https://github.com/zavolanlab/htsinfer, while releases are published on Bioconda. A snapshot of the HTSinfer version described in this article was deposited at Zenodo at 10.5281/zenodo.13985958.