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Getting started

The service is currently available in beta-version for free. We would be grateful for any positive or negative feedback from you to make the service better. Please leave it using the Feedback button.

You can get overview of all features and see sample analytical reports for several published datasets. To view them, please login in demo mode using the following credentials: login demo@knomics.ru, password knomicsdemo (view-only).

To analyze your own metagenomes, please complete the following steps (Note: currently only 16S rRNA sequencing data format is supported).

  1. Register an account through “Sign Up” section.
  2. Sign in and create a new project in your account. A single project is intended to contain all metagenomes from one study.
  3. Open the project on Projects page and upload your metagenomic datasets. Available input formats are FASTQ and FASTA (or their archives). The reads should be uploaded in a “one file-one sample” way. You can run Basic report and External comparison reports now.
  4. If you want to analyze the links between microbiota composition with various factors (in Case-control, Factor analysis or Meta-analysis reports), please upload a metadata file in delimited values format (details are below). The file should be uploaded through the same section as metagenomic data.
  5. Run one or several of the desired analyses.
  6. Analysis status (Processing, Scheduled, Ready or Error) is displayed at the Project page.
  7. After the analysis is complete, you can view its results as an interactive report.
  8. If you want to share the report, press the “Share report” button and send the public link to anyone. You can also press the same button to cancel the sharing.
  9. If the analysis produces Error status and the message is not self-explanatory, please contact us using the Feedback button. We will react as soon as possible.

Preparing your metadata file

Metadata - additional information about each sample (age, body-mass index, clinical status, etc.) - should be uploaded as a delimited text file, with each column corresponding to a single factor and each row - to a single row. The delimiter can be comma, tab or custom symbol.

Generally, the metadata file should contain at least 1 column - IDs of samples - with reserved name “sample”. Each name should be the same as the filename of the respective readset without extension. However, if this word ends with _R1 or _R2 (typical for output of Illumina sequencer), these should be excluded from sample IDs in metadata. During analysis, all “_” symbols will be substituted with “.” symbols. Examples of filnames and expected sample names in the metadata file: SRS1234.fastq.gz - SRS1234, SRS5678_R1.fastq.gz - SRS5678.

If you want to analyze 2 groups of samples within your data (Case-Control analysis), the metadata should include at least 2 columns: sample IDs and information about membership of each sample in case or control group (in a column with reserved name “case_control”). The latter column can include one of the two values: “case” or “control”.

If you want to analyze your metagenomes and metadata in comparison with external metagenomes and metadata (Meta-analysis), it is possible to use the following factors (and reserved column names) provided for all external datasets:

  • sample - sample ID
  • age - age of the subject, in years
  • gender - M or F
  • bmi - body-mass index
  • icd10 - disease of the subject, according to the International Classification of Diseases (e.g., G06.1, A06.9)
  • country - for example, Russia, USA
  • case_control - as described above (can be equal to one of two values - case or control)
  • antibiotics - logical value indicating whether subject had recent undergone antibiotic therapy (can be equal to “true” or “false”)