BaseClear offers dedicated metagenomics and metatranscriptomics services to answer two fundamental questions in microbial diversity studies – “what microbial species are there?” and “what are they doing?”.

Metagenomics analysis allows the exploration of the diversity, composition and functional capacity of microbial communities. With the development of next-generation sequencing technologies and advances in bioinformatics and biostratistics, studying metagenomic communities delivers increasingly valuable data and insights . Our experts are happy to discuss the details and best technical approach that can be used to answer the research questions with your next metagenomics or metatranscriptomics projects.

Metagenomics sequencing analysis

Our state-of-the-art shotgun metagenomics sequencing pipeline covers all aspects for metagenome analysis. This starts with the quality control of the data, and includes metagenome assembly and the generation of tables that describe the abundance of different functional units, such as KEGG KOs and pathways, across different samples. To this end, we use an in-house, improved analysis suite that includes metagenome assembly, gene prediction, gene catalogue creation and annotation, as well as abundance estimation of annotated genes and other functional units.

In addition, we use a highly accurate and robust method to deduce taxonomic profiles from metagenomics data. These results are not only summarised (in tables) and visualised (in cladograms) per sample and per project, but can also be visualized in our genome explorer to accelerate the interpretation of results by our clients.

Output for metagenomics analysis projects

  • A de novo metagenomics sequencing assembly per sample.
  • Gene predictions and their protein translations in FastA as well as GenBank formats.
  • A non-redundant gene catalogue that is created by clustering the predicted genes (can be done both at sample and at project-level), providing an inventory of the gene content.
  • Annotation of the gene catalogue with more than 10 databases and functional units including KEGG orthologous groups, modules, pathways, as well as COGs.
  • Functional profiling (abundance) tables of non-redundant genes and KEGG KOs, modules, pathways, and COGs. Both raw and normalised abundances are provided.
  • Taxonomic relative abundance profiles per sample and per project both in BIOM format and Excel-sheet format, accompanied by corresponding cladogram figures.
Request a quotationContact our experts

Metatranscriptomics analysis

While metagenomics analysis provides a wealth of knowledge with respect to the functional potential of the sampled microbial community, it does not provide information about which of these functions are expressed. The latter can be achieved by metatranscriptomics and starts with the extraction of RNA. As the extracted RNA predominantly consists of non-coding RNAs (e.g. ribosomal RNA) that do not give information about functional expression, an rRNA depletion step is performed. This is followed by library preparation and paired-end sequencing on the Illumina platform. BaseClear offers complete solutions for metatranscriptomics research and applications.

Metatranscriptomics services
Researchers looking at NGS services results

Convinced? Get in touch

Get a quoteMeet baseClearContact form