FragGeneScan.rs: Rust Implementation of FragGeneScan

This repository contains a Rust implementation of the popular FragGeneScan utility. It fixes many common race conditions and parallellism issues with the original FragGeneScan-tool and improves upon code quality.

Technologies used

• Rust
• Rayon
• Rust-Bio
• Clap
• Whiteread (for parsing the FragGeneScan input files)

Usage

To build the project:

cargo build

To make a release build of the project:

cargo build --release

Get the utility's help documentation

./fgsrs --help

Process one of the example files (output of FragGeneScan 1.31 is also present in the /example folder):

./fgsrs -w 0 -p 20 -t train/454_10 < example/NC_000913-454.fna > NC_000913-454-fgs.faa 

License

FragGeneScan.rs is made available under the MIT License. Reference to the author and this repository however is appreciated.

References

Based upon the original implementation:

Mina Rho, Haixu Tang, and Yuzhen Ye. FragGeneScan: Predicting Genes in Short and Error-prone Reads. Nucl. Acids Res., 2010 doi: 10.1093/nar/gkq747