The raw sequence data, produced by DNA sequencers, contains the genomic information of the microbes present in your samples. Still, it also includes non-biological sequences such as primers, barcodes, and low-quality DNA bases. These need to be filtered out before continuing analysis. These preprocessing steps are required for all sequence data types. This includes 16S/18S/ITS and other PCR amplicons, whole genomes, and shotgun metagenomes.

After filtering out non-biological and low-quality sequences, the genomic information in the sequence data can be utilized to identify sequencing reads that are likely coming from the same organism and to calculate the organism's abundance in your samples. This step can be done using several different methods, depending on your individual needs. We can, for example, identify groups of organisms on species or single nucleotide variant levels.

After grouping sequences from the same organism, we can give the organism a name and a place in the tree of life. The mapping can be done against any chosen sequence database. For 16S/18S rRNA gene amplicon sequences, SILVA is a good choice. For species or strain profiling of whole genome and metagenome samples, there are also many choices, such as ChocoPhlAn3.

We also provide identification of functional genes of the whole genome and metagenome samples. In addition to metabolic genes or pathways, specific annotations can be done such as identifying antibiotic resistance genes or virulence factors.

Sequencing projects using PCR amplification are prone to have some levels of contaminating sequences that are not coming from your samples or cross contamination, meaning that the sequences coming from different samples are mixed. Therefore, a prudent decontamination step is crucial for obtaining data that you can trust. We offer decontamination based on automation. Still, we always also check the contamination manually to provide reliable results.