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SciBear: Bearing the knowledge


The SciBear team analyzes all types of microbial genome sequencing data. We provide efficient, quick and reliable analysis of your data. Our specialized SciBear analysis report is designed to be readily incorporated into scientific manuscripts.

New microbial species are discovered almost every day. High-quality assembly and annotation of the microbial genome are the foundation of successful future research. SciBear has developed a pipeline for de novo assembly and annotation of microbial genomes. Raw DNA sequencing reads is the only input we need from you. We will perform a quality check on your DNA reads, assemble the microbial genome and analyze it for completeness and potential contamination. We will define the taxonomic position of the assembled genome and its average nucleotide identity (ANI) with the nearest microbial genome. We will annotate the genome, evaluate CRISPRs, and analyze COGs and Pfam domains. Your SciBear report will provide results corresponding to the minimum information about the genome sequence (MIGS) specification (doi: 10.1038/nbt1360).

De novo assembly and annotation of microbial genomes

genome assembly
For the investigation of microbial communities, SciBear has developed a pipeline for microbiome analysis using a metagenomic approach. If genetic material was extracted directly from environmental or host-associated samples, metagenomic analysis is required for the investigation of the microbial communities.

The composition of the microbial community and its functional potential can be determined based on microbial DNA recovered from samples. Raw DNA sequencing reads is the only input we need from you. After a quality check and reads cleaning, we assemble and annotate the metagenome to determine the metabolic capabilities of the analyzed community.

To reconstruct the microbial genomes (Metagenome-Assembled Genomes or MAGs) of a given sample, we carry out binning of the metagenome using at least three different methods.

Metagenomic analysis of microbiomes

metagenomic analysis
The pan-genomic analysis is the newest approach allowing to decipher the entire gene content within the set of genomes. Pan-genomic analysis presents all the gene variability of a group of organisms. Pan-genomic analysis can be used to find homologous genes and predict the metabolic properties of a microorganism. The pan-genomic analysis shows the diverse genomic features explaining a range of microbial adaptations to various environments. The pan-genomic analysis is essential for proper taxonomy or reclassification of the species.

We are happy to help you with the pan-genomic analysis of microorganisms of your interest. To carry out this analysis, we only need information about the group of microbes whose genomes you wish to compare, and which metabolic pathways are of particular interest.

Microbial pan-genome analysis

pan-genome analysis
Evolutionary relationships between different microbe species are based can be explained by phylogenetic analysis.Phylogenetic characterization is crucial for contextualizing genomes without prior phenotypic information, and for determining their genetic novelty and genotype-phenotype relationships. SciBear's team has vast experience both in reclassifying existing and describing new microbial taxa, as evidenced by publications in specialized journals such as the International Journal of Systematic (IJSEM) and Evolutionary Microbiology and Bergey's Manual of Systematics of Archaea and Bacteria (BMSAB). We are happy to share our experience and help you with phylogenetic analysis. The subject of analysis can be phylogenetic markers (e.g. 16S rRNA), concatenated single-copy core genes of analyzed genomes, or any gene or group of genes of interest.

Microbial phylogenetics

microbial phylogenetic
Send us your data
Now relax and let us do the work
Your results!
As soon as we have a clear idea of which output format you want, we'll request your raw data to get started. Your sequencing results can be shared with us in any way convenient for you (for example, through a link to Dropbox, by FTP, etc.)

Your report will be generated within 3 days! While you wait, you can plan your next research project and think about big scientific ideas.
Your results will be delivered in the form of a FASTA file containing your genome assembly, a brief report with the main outcomes, and a detailed report (you can see a sample report here)
Just fill in the form with the key information about your request, and we will reply to you as soon as possible. Feel free to ask any questions by e-mail to:
Just press the "order now" button and fill in the form


PhD in Biology (Lomonosov Moscow State University)

Specialist in microbial genomics, systematics, and evolution. Co-author on more than 80 publications in peer-reviewed scientific journals.

Master of Applied Mathematics and Informatics (Moscow Institute of Physics and Technology)

Bioinformatics analyst, software engineer. Co-author on more than 20 publications in peer-reviewed scientific journals.

Master of Science in Biology (Lomonosov Moscow State University)

Biologist, specialist in project management. Co-author of 5 patents.


Master of Science in Finance and Supply Chain Management (Plekhanov Russian University of Economics)

Sourcing Professional with 5 years of experience in supply chain practices for different groups of commodities.


AA Nikitina, AY Kallistova, DS Grouzdev, TV Kolganova, AA Kovalev, DA Kovalev, V Panchenko, I Zekker, AN Nozhevnikova, YV Litti
Syntrophic butyrate-oxidizing consortium mitigates acetate inhibition through a shift from acetoclastic to hydrogenotrophic methanogenesis and alleviates VFA Stress in thermophilic anaerobic digestion
Applied Sciences. 2023; 13(1):173. doi:10.3390/app13010173