FNBtools

FNBtools identifies homozygous causal deletions in mutant populations from next-generation sequencing (NGS) data to enable mapping of genotype–phenotype relationships.

Key Features:

• Population-scale deletion detection: Identifies homozygous deletions across entire mutant populations using NGS data.
• High accuracy across coverage levels: Maintains high sensitivity and specificity across different sequencing coverage levels.
• Detection of small and large deletions: Detects both small and large deletions that are causal in mutant populations.
• Unique deletion identification: Filters out deletions present in wild-type or control pools to pinpoint unique deletions within mutant pools.
• Genome-wide visualization: Produces Circos-based genome-wide visualizations of identified deletions.
• Benchmarking performance: Outperforms existing popular deletion callers for small-deletion detection across coverage levels as demonstrated by simulated-data analyses.

Scientific Applications:

• Functional genomics and genetics: Facilitates forward and reverse genetics studies using deletion mutagenesis methods such as fast neutron bombardment (FNB) to link deletions to phenotypes.
• Case study—Medicago truncatula salt tolerance: Applied to a salt-tolerant Medicago truncatula mutant to identify a unique deletion locus that was validated by PCR amplification, sequencing, and genetic linkage analyses.

Methodology:

Analyzes NGS data to detect homozygous deletions at population scale, filters deletions against wild-type/control pools to identify unique events, generates Circos visualizations, and was benchmarked using simulated-data analyses showing improved sensitivity and specificity for small and large deletions.