VARUS was originally written by Willy Bruhn as a Bachelors' thesis supervised by Mario Stanke. This repository is a copy of https://github.com/WillyBruhn/VARUS made in November 2018 and contains many bugfixes, an incremental intron database feature and an extension for using HISAT al alternative alignment program.

VARUS automates the selection and download of a limited number of RNA-seq reads from at NCBI's Sequence Read Archive (SRA) targeting a sufficiently high coverage for many genes for the purpose of gene-finder training and genome annotation. Each iteration of the online algorithm

• selects a run to download that is expected to complement previously downloaded reads
• downloads a sample of reads ("batch") from the run with fastq-dump
• aligns the reads with STAR or HISAT
• evaluates the alignment

Invoke the following command from the command-line in order to clone the repository:

git clone https://github.com/MarioStanke/VARUS.git

VARUS depends on

• samtools,
• bamtools, install on Ubuntu with sudo apt-get install bamtools libbamtools-dev
• fastq-dump and
• STAR or HISAT2 (tested with HISAT 2, version 2.0.0-beta)

Compile VARUS manually with

cd Implementation
make

By default the NCBI tool fastq-dump creates temporary files under ~/ncbi of the same size as the run file from which data is downloaded, even if only a small part thereof is downloaded. Disable this caching behavior that requires probably too much hard drive space for most users with

mkdir -p ~/.ncbi
echo '/repository/user/cache-disabled = "true"' >> ~/.ncbi/user-settings.mkfg

Change to directory example and follow the instructions in example/README.

Copy the file VARUSparameters.txt from the example folder to your working directory and adjust it if necessary:

Most important parameters:

--batchSize specifies how many reads should be downloaded in each iteration (e.g. 50000 or 200000)

--maxBatches specifies how many batches should be downloaded at most

The final output is a sorted spliced alignment file (all batches together) called VARUS.bam.

Please cite: VARUS: sampling complementary RNA reads from the sequence read archive. 2019; BMC Bioinformatics, 20:558

Find the bachelor thesis of Willy Bruhn corresponding to VARUS in /docs/Thesis.