LAMPS: an analysis pipeline for sequence-specific ligation-mediated amplification reads

• Published in: BMC research notes Vol. 13; no. 1; p. 273
• Main Authors: Cameron, Christopher J F, Wang, Xue Q D, Dostie, Josée, Blanchette, Mathieu
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 03-06-2020; BioMed Central; BMC
• Subjects: Analysis; Bias; Bioinformatics; Bioinformatics pipeline; Carbon; Carbon copy-chromatin immunoprecipitation; Chromatin; Chromatin Immunoprecipitation; Chromosome Conformation Capture Carbon Copy; Chromosomes; Computational biology; Computer applications; Conformation; Data analysis; Deoxyribonucleic acid; DNA; DNA sequencing; Gene amplification; Gene Library; Gene mapping; Genomes; High-Throughput Nucleotide Sequencing - methods; Humans; Immunoprecipitation; Integration; Methods; Multiplex Polymerase Chain Reaction - methods; Multiplexed ligation-mediated amplification; Nucleic Acid Amplification Techniques - methods; Nucleotide sequence; Operating systems; Polymerase chain reaction; Protocol; Quality Control; Research Note; Sequence Analysis, DNA - methods; Software; Canada; Carbon copy-chromatin immunoprecipitation; Bioinformatics pipeline; Multiplexed ligation-mediated amplification; Chromosome Conformation Capture Carbon Copy
• ISSN: 1756-0500; 1756-0500
• DOI: 10.1186/s13104-020-05106-1

Ligation-Mediated Amplification (LMA) is a versatile biochemical tool for amplifying selected DNA sequences. LMA has increased in popularity due to its integration within chromosome conformation capture (5C) and chromatin immunoprecipitation (2C-ChIP) methodologies. The output of either 5C or 2C-ChIP protocols is a single-read sequencing library of ligated primer pairs that may or may not be multiplexed. While many computational tools currently exist for read mapping and analysis, these tools neither fully support multiplexed libraries nor provide qualitative reporting on the LMA primers involved. Typically, the task of library demultiplexing or primer analysis is offloaded on to the user. Our aim was to develop an easy-to-use pipeline for processing (multiplexed) single-read sequencing data produced by sequence-specific LMA.
Here, we describe the Ligation-mediated Amplified, Multiplexed Primer-pair Sequence (LAMPS) analysis pipeline. LAMPS facilitates the analysis of multiplexed LMA sequencing data and provides a thorough assessment of a library's reads for a variety of experimental parameters (e.g., primer-pair efficiency). The standardized output of LAMPS allows for easy integration with downstream analyses, such as data track visualization on a genome browser. LAMPS is made publicly available on GitHub: https://github.com/BlanchetteLab/LAMPS.