ArticleBMC bioinformatics2022
FragGeneScanRs: faster gene prediction for short reads.
Article in BMC bioinformatics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- ChloroScan: Recovering Plastid Genome Bins From Metagenomic Data.Molecular ecology resources · 2026Article
- Carbon regime structures functional trait trajectories during primary succession in microorganisms.The ISME journal · 2026Article
- Precipitation legacy effects on soil microbiota facilitate adaptive drought responses in plants.Nature microbiology · 2025Article
- Computational function prediction of bacteria and phage proteins.Microbiology and molecular biology reviews : MMBR · 2025Review
- A defined microbial community reproduces attributes of fine flavour chocolate fermentation.Nature microbiology · 2025Article
- ProteoSeeker: A Feature-Rich Metagenomic Analysis Tool for Accessible and Comprehensive Metagenomic Exploration.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- GSearch: ultra-fast and scalable genome search by combining K-mer hashing with hierarchical navigable small world graphs.Nucleic acids research · 2024Article
- MetaCerberus: distributed highly parallelized HMM-based processing for robust functional annotation across the tree of life.Bioinformatics (Oxford, England) · 2024Article
- MerCat2: a versatileBioinformatics advances · 2024Article
- Homing in on the rare virosphere reveals the native host of giant viruses.bioRxiv : the preprint server for biology · 2023Article
- Benchmarking Community-Wide Estimates of Growth Potential from Metagenomes Using Codon Usage Statistics.mSystems · 2022Article
- UMGAP: the Unipept MetaGenomics Analysis Pipeline.BMC genomics · 2022Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
backgroundFragGeneScan 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.
resultsThis 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.
conclusionsCompared to the current C implementation, shotgun metagenomic reads are processed up to 22 times faster using a single thread, with better scaling for multithreaded execution. The Rust code of FragGeneScanRs is freely available from GitHub under the GPL-3.0 license with instructions for installation, usage and other documentation ( https://github.com/unipept/FragGeneScanRs ).
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.