FGMP

FGMP assesses fungal genome completeness using evolutionary conserved sets of proteins and DNA elements to evaluate both assembled genomes and unassembled reads for genomic data integrity.

Key Features:

• Evolutionary conserved sets: Utilizes evolutionary conserved sets of proteins and DNA elements to assess genome completeness.
• Applicability to data types: Operates on both assembled genomes and unassembled reads.
• Benchmarking: Demonstrated accuracy and reliability in a comparative analysis involving 246 fungal genome assemblies against existing methods.
• Assembly update assessment: Identified improvements or degradations in genome assembly quality across 57 updated fungal assemblies recorded in the NCBI assembly archive.

Scientific Applications:

• Genome completeness quantification: Provides completeness measures to support biological interpretation and comparative genomics, including evaluation of reported patterns such as high rates of gene loss.
• Analysis of unassembled reads: Enables direct analysis on unassembled reads to reduce sequencing costs and facilitate studies of non-model fungal organisms.

Methodology:

Uses evolutionary conserved sets of proteins and DNA elements to assess completeness; accepts assembled genomes and unassembled reads; benchmarked via comparative analysis on 246 fungal genome assemblies and evaluated assembly updates in 57 cases from the NCBI assembly archive.