LAMPS

LAMPS analyzes sequence-specific Ligation-Mediated Amplification (LMA) reads to process and evaluate multiplexed single-read sequencing data from 5C and 2C-ChIP experiments.

Key Features:

• Multiplexed Library Support: Handles multiplexed single-read sequencing libraries derived from LMA and automates demultiplexing of pooled samples.
• Primer-Pair Efficiency Assessment: Reports qualitative assessments of LMA primer-pair efficiency to evaluate experimental performance.
• Standardized Output: Produces standardized output formats compatible with downstream analyses and genome browser track visualization.

Scientific Applications:

• 5C (chromosome conformation capture): Processes LMA-derived reads to support analysis of spatial genome organization using 5C data.
• 2C-ChIP (chromatin immunoprecipitation): Processes LMA-derived reads to support analysis of protein–DNA interactions from 2C-ChIP experiments.
• Epigenetics and gene regulation studies: Provides standardized, primer-aware read assessments to inform studies of epigenetic state and transcriptional regulation.

Methodology:

Processes single-read sequencing libraries derived from ligated primer pairs, demultiplexes multiplexed libraries, assesses primer-pair efficiency, and outputs standardized files for integration with downstream bioinformatics tools and genome browser visualization.