VARUS

VARUS is a software tool that automates selecting, downloading, and aligning RNA-Seq data from NCBI's Sequence Read Archive (SRA) for a given species and genome. Its main features and advantages include:

1. Automated data selection: VARUS chooses the most suitable RNA-Seq runs from the SRA, eliminating the need for manual selection.

2. Efficient data sampling: The tool employs an online algorithm to randomly select subsets of reads, aiming to cover a large number of transcripts adequately while considering limited network bandwidth and computing resources.

3. Improved sensitivity and specificity: VARUS achieved better sensitivity and specificity in most tested species with fewer downloaded reads compared to manual run selection.

4. Compatibility with genome annotation tools: RNA-Seq data sampled with VARUS is well-suited for fully automatic genome annotation using tools like BRAKER.

5. Automation of genome annotation: VARUS enables the complete automation of the genome annotation process, including the selection and quality control of RNA-Seq data, without compromising accuracy compared to manually supervised annotation.