The ever-increasing use of multi-omics investigations has become a pivotal and major technique for decoding complex biological systems. These high-throughput technologies produce a mammoth load of data in comparison to analysing just one layer of data and are frequently constrained by the type and variety of data being analysed. However, the use of multi-omics data integration strategies allows researchers to correlate cellular function levels, including genomes, epigenomes, transcriptomes, proteomes, modified proteomes, metabolomes, lipidomics, microbiomes and phenomes, this helps in data analysis and interpretation to elucidate the underlying mechanism of biological processes. This chapter provides detailed information on state-of-the-art analytical tools used in modern research of omics, particularly on computational techniques for amalgamating various omics data layers. We have covered algorithms, analytical pipelines, and web-based multi-omics integration tools available for data analysis and visualization. In addition, we have also conducted a concise review of multi-omics studies available to date for high-altitude acclimatization and maladaptation.