cogeqc

Workflows

Standard Workflow

Assess genome assembly and annotation quality by comparing custom statistics against NCBI genomes and evaluating gene space completeness with BUSCO.

library(cogeqc)

# 1. Retrieve and compare genome assembly statistics
maize_stats <- get_genome_stats(taxon = "Zea mays")
my_stats <- data.frame(
    accession = "my_lovely_maize",
    sequence_length = 2.4 * 1e9,
    gene_count_total = 50000,
    CC_ratio = 2
)
comparison <- compare_genome_stats(ncbi_stats = maize_stats, user_stats = my_stats)
plot_genome_stats(ncbi_stats = maize_stats, user_stats = my_stats)

# 2. Read and plot BUSCO summary statistics
output_dir <- system.file("extdata", package = "cogeqc")
busco_summary <- read_busco(output_dir)
plot_busco(busco_summary)

Input: Custom genome assembly statistics and BUSCO output directories; Output: Quality control comparison tables and summary visualization plots.

When to Use

• Assessing genome assembly and annotation quality by comparing custom statistics against NCBI genomes using get_genome_stats, compare_genome_stats, and plot_genome_stats.
• Assessing gene space completeness using BUSCO via run_busco, read_busco, and plot_busco.
• Assessing orthogroup inference (e.g., from OrthoFinder or OrthoMCL) using a protein domain-based approach with read_orthogroups and assess_orthogroups.

When NOT to Use

• For performing the actual genome assembly, gene annotation, or orthogroup clustering itself. Use external tools like Flye, Liftoff, or OrthoFinder, then use cogeqc for downstream quality control.

Data Requirements

• For genome stats: A data frame of user-defined assembly statistics containing at least an accession column and other matching NCBI fields (e.g., sequence_length, gene_count_total, CC_ratio).
• For BUSCO: A directory containing BUSCO output files or pre-parsed BUSCO summary data frames.
• For orthogroups: An OrthoFinder Orthogroups.tsv file or a parsed data frame with columns Orthogroup, Species, and Gene.

Key Parameters

• taxon (NULL): Taxon name or NCBI Taxonomy ID to retrieve statistics for in get_genome_stats.
• filters (NULL): List of key-value pairs to filter NCBI Datasets API results in get_genome_stats.
• ncbi_stats (NULL): Reference data frame of NCBI genome statistics in compare_genome_stats and plot_genome_stats.
• user_stats (NULL): Data frame of user-observed genome statistics to compare or highlight.
• lineage (NULL): Lineage dataset name for BUSCO in run_busco.
• mode (NULL): BUSCO run mode (e.g., "genome") in run_busco.
• outpath (NULL): Path to directory where BUSCO output will be stored in run_busco.
• download_path (NULL): Path to directory where BUSCO datasets will be downloaded in run_busco.

Best Practices

• Use the CC_ratio (ratio of contigs to chromosome pairs) as a robust measurement of contiguity that allows cross-species comparisons.
• Filter NCBI reference genomes to match your assembly level (e.g., chromosome-scale) and annotation status using the filters parameter in get_genome_stats.
• Check if BUSCO is installed in your PATH using busco_is_installed before calling run_busco.
• Consider genomes with >90% complete BUSCOs as high quality when visualizing with plot_busco.

Common Pitfalls

• run_busco failing due to missing system dependencies. Fix: Ensure BUSCO is installed and in your system PATH, or check with busco_is_installed().
• Column mismatch when comparing custom stats with NCBI stats. Fix: Ensure the column names in your custom data frame exactly match the column names returned by get_genome_stats (e.g., sequence_length instead of genome_size).

Alternatives

• quast (external tool) for general genome assembly quality metrics.
• OrthoFinder (external tool) for orthogroup inference.

Citations

• Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM (2015). BUSCO: Assessing Genome Assembly and Annotation Completeness with Single-Copy Orthologs. Bioinformatics.
• Wang P, Wang F (2022). A Proposed Metric Set for Evaluation of Genome Assembly Quality. Trends in Genetics.

References

• Homepage: bioconductor.org/packages/cogeqc
• Vignette: https://bioconductor.org/packages/release/bioc/vignettes/cogeqc/inst/doc/genome_assembly_annotation_completeness.html