qc3C

qc3C estimates the proportion of proximity-ligation-derived signal in Hi-C DNA sequencing libraries using reference-free k-mer analysis.

Key Features:

• Reference-free quality assessment: Operates without a reference genome to evaluate Hi-C library quality.
• Proximity ligation event detection: Identifies k-mers generated by Hi-C proximity ligation events that are unlikely to occur naturally in the sample.
• Signal proportion estimation: Quantifies the proportion of "signal" within a Hi-C library as an indicator of data quality.
• Dual QC capabilities: Also supports reference-based quality control when a reference genome is available.
• Low data requirement: Characterizes Hi-C library quality from only a modest amount of sequencing data.

Scientific Applications:

• 3D chromatin structure analysis: Enables assessment of Hi-C data quality for studies of chromosomal architecture.
• Genome scaffolding: Informs use of Hi-C contacts for scaffolding large genome assemblies.
• Metagenome-assembled genome (MAG) resolution: Supports quality assessment of Hi-C libraries used to resolve genomes from environmental and metagenomic samples.

Methodology:

qc3C analyzes k-mers produced by Hi-C proximity ligation events, distinguishes these ligation-derived k-mers from naturally occurring sequences, and estimates the proportion of "signal" in a Hi-C library; the approach requires only a modest amount of sequencing data and has been validated on simulations and real datasets.