sbludwig/rastair repository overview

⁠Rastair 2

Rastair is a CLI application that allows the simultaneous detection of genetic variants and methylated positions from short-read sequencing data created using TET-Assisted Pyridine-Borane Sequencing (TAPS)⁠, Illumina 5-Base sequencing⁠ or any other method that converts 5mC to T.

⁠Installation

⁠From Source

To build rastair, you'll need:

• Rust (version 1.88 or later)
• libclang-dev and cmake

Then you can build it with:

cargo xtask release

⁠Binary releases

We provide binary releases for Linux and Mac. Visit www.rastair.com⁠ for details.

⁠Docker

You can install the pre-built docker image in the usual way. For example, to install version 2.1.1, you could do:

docker pull sbludwig/rastair:version-2.1.1

⁠Usage examples

⁠1. Call genomic variants and methylated positions at all genomic positions

rastair call -r reference.fa.gz -o test.vcf.gz test.bam

⁠2. Only call methylation at CpGs and variants that generate a CpG

rastair call -r reference.fa.gz --bed test.bed.gz test.bam

This is significantly faster than calling variants across all genomic loci, but still runs the ML-based variant caller.

⁠2. Call methylation at CpGs without ML filtering (ultra-fast)

rastair call --no-ml -r reference.fa.gz --bed test.bed.gz test.bam

This will be very similar to the output from other methylation callers.

⁠Contributing

If you want to contribute, please read the CONTRIBUTING.md⁠ file. To start coding, have a look at the xtask documentation⁠.

⁠License

This software is made available under a "non-commercial-use" license. Please refer to LICENSE.txt for details.