FragGeneScanRs: faster gene prediction for short reads.

ABSTRACT:

Background

FragGeneScan is currently the most accurate and popular tool for gene prediction in short and error-prone reads, but its execution speed is insufficient for use on larger data sets. The parallelization which should have addressed this is inefficient. Its alternative implementation FragGeneScan+ is faster, but introduced a number of bugs related to memory management, race conditions and even output accuracy.

Results

This paper introduces FragGeneScanRs, a faster Rust implementation of the FragGeneScan gene prediction model. Its command line interface is backward compatible and adds extra features for more flexible usage. Its output is equivalent to the original FragGeneScan implementation.

Conclusions

Compared to the current C implementation, shotgun metagen

SUBMITTER: Van der Jeugt F 

PROVIDER: S-EPMC9148508 | biostudies-literature | 2022 May

REPOSITORIES: biostudies-literature