NCBI fcs

NCBI fcs identifies and removes contaminant sequences from genome assemblies to improve assembly quality for research and database submission.

Key Features:

• FCS-GX rapid screening: FCS-GX is optimized for rapid screening of new genome assemblies, operating in roughly 0.1 to 10 minutes per genome.
• Empirical evaluation: Performance was tested on artificially fragmented genomes and demonstrated high sensitivity and specificity across diverse contaminant species.
• Large-scale screening: Applied to ~1.6 million GenBank assemblies, the suite identified 36.8 Gbp of contamination (≈0.16% of bases), with half of that contamination arising from 161 assemblies.
• RefSeq improvement: Implementation of FCS-GX in NCBI RefSeq assembly updates reduced detected contamination to 0.01% of bases.

Scientific Applications:

• Genome assembly quality control: Detection and removal of non-source contaminant sequences to improve accuracy of assembled genomes intended for analysis and submission to repositories such as GenBank.
• Repository curation: High-throughput screening to quantify and reduce contamination across large public assembly collections including GenBank and NCBI RefSeq.
• Method validation: Benchmarking sensitivity and specificity using artificially fragmented genomes to assess contaminant detection performance across diverse species.

Methodology:

FCS-GX performs rapid computational screening of genome assemblies (0.1–10 minutes per genome), was evaluated on artificially fragmented genomes for sensitivity and specificity, and was applied to screen ~1.6 million GenBank assemblies identifying 36.8 Gbp (≈0.16%) of contamination and reducing RefSeq contamination to 0.01% of bases.