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Quick Start

This guide will get you up and running with BUSCOlite in just a few minutes.

Installation

First, install BUSCOlite:

pip install buscolite

Or using conda:

conda install -c bioconda buscolite

Download a BUSCO Lineage

Download the appropriate lineage for your organism from the BUSCO website:

# Example: Download the fungi lineage
wget https://busco-data.ezlab.org/v5/data/lineages/fungi_odb10.2020-09-10.tar.gz
tar -xzf fungi_odb10.2020-09-10.tar.gz

Run BUSCO Analysis

Genome Mode

Analyze a genome assembly:

buscolite -i genome.fasta -o mygenome -m genome -l fungi_odb10 -c 8 -s anidulans

This will:

  • Analyze genome.fasta using the fungi lineage
  • Use 8 CPU threads
  • Use the anidulans Augustus species model
  • Generate output files with prefix mygenome

Protein Mode

Analyze a protein set:

buscolite -i proteins.fasta -o myproteins -m proteins -l fungi_odb10 -c 8

Generate Plots

After running the analysis, you can generate publication-quality SVG plots:

Single Sample Plot

buscolite-plot mygenome.buscolite.json -o mygenome_plot.svg

Multi-Sample Comparison

Compare multiple BUSCO results:

buscolite-plot sample1.buscolite.json sample2.buscolite.json sample3.buscolite.json -o comparison.svg

Understanding the Output

BUSCOlite generates three main output files:

  1. <output>.buscolite.json - Comprehensive results in JSON format including:
  2. Version and mode information
  3. Lineage configuration
  4. Statistics (complete, duplicated, fragmented, missing)
  5. Detailed results for each BUSCO

  6. Command used

  7. <output>.buscolite.tsv - Tab-separated summary table

  8. <output>.buscolite.gff3 - GFF3 annotations (genome mode only)

Next Steps