When a methods section says “assembled with SPAdes” or “classified with Kraken2,” reviewers know exactly what that means. Those tools are the standard, but they are command-line programs. They are awkward to install on Windows, they need a lot of memory, and some cannot realistically run on a laptop at all.
Omi can now run them for you on a cloud server. You describe the task and the files, Omi runs the right tool, then brings back the results and reports.
The toolbox
- Quality control: FastQC, fastp, Trimmomatic
- Typing and lineage: mlst, Nextclade, Pangolin
- Assembly and mapping: SPAdes, Flye, read mapping
- Variants: FreeBayes, SnpEff
- Metagenomics: Kraken2, Bracken, Krona charts
- Phylogenetics: IQ-TREE
Tools can be chained. For example, you can map reads, call variants on the result and annotate them without re-uploading anything between steps.
How researchers can use it
- Bacterial isolates: check read quality, assemble with SPAdes for short reads or Flye for long reads, then type the isolate with mlst.
- Outbreak and viral work: assign lineages with Pangolin or Nextclade, then build a tree with IQ-TREE.
- Variant calling: map reads, call variants with FreeBayes and annotate them with SnpEff.
- Metagenomics: classify shotgun reads with Kraken2 and Bracken and get an interactive Krona chart.
For quality control, Omi reads the report and tells you each module’s pass, warn or fail verdict plainly, and the full report opens in the app.
Why the cloud matters
- Your laptop no longer decides your method. Assembly and metagenomic classification can need many gigabytes of memory.
- Large files are handled carefully. Very large result files stay in your cloud workspace instead of being forced onto your machine.
- Long jobs do not tie up your computer. They run on the server while you keep working.
- Your methods section stays standard. You can cite the same tools reviewers already know.
Honest limits
- The Kraken2 database is a reduced one, so a share of reads stays unclassified.
- GATK is not available yet. FreeBayes covers small genomes such as bacteria and viruses.
- The server is shared, so very large jobs may queue.
Good to know: cloud tools need a paid plan or a One-Time Project Access top-up, and Omi asks your permission before it uploads your files.
Get it
Download version 1.5.47 for Windows from the download section. If you tried a tool on your own data, tell us how it went at info@omicsboard.com. To read about cloud R, see Cloud R and cloud analysis.