ABSTRACT
In the past few decades, there has been a significant development in the sequencing technologies, which has accelerated the research to study complex microbiomes. Although 16S rRNA analysis and diversity analysis at species level are most commonly used, researchers are making a shift towards using more comprehensive sequencing methods such as metagenomics (sequencing of total DNA—revealing which microbes are present) and metatranscriptomics (sequencing of total RNA—capturing all gene expression). Integrating these two levels of information provides a more robust method for understanding the mechanisms of a microbial community. However, such multi-omics data poses new challenges and create new scientific questions that are still to be answered. In this chapter, we will try to summarize the recently updated databases, which host these sequencing data from the microbial populations. We will also provide a survey of algorithms and tools used for building genome/transcriptome assembly along with its annotation. We will then conclude with a discussion on specific challenges posed by multi-omics data and outline some of the strategies recently developed to address these complexities.
