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Launching Genome Assemblies
Denise Lynch avatar
Written by Denise Lynch
Updated over a week ago

The Genome Library is a premium feature on the One Codex platform, allowing users to generate assemblies, annotate the genomes, store and search across your genomes. Here, we'll walk you through launching genome assemblies from your samples on One Codex.

Upload Your Samples

To get started, upload your raw sequence data as samples to the One Codex platform. If you have both short- and long-read data, upload them as separate samples.

Launch an Assembly

Visit the "Run Analyses" page, and select the raw read sample you wish to assemble from. If you wish to generate hybrid assemblies, select one of your samples. You will later be presented with an opportunity to provide the matching sample.

At the bottom of the Run Analyses page, you will see a section for Assembly. Choose your appropriate assembly method for your organism. Options include:

  • De Novo Bacterial Genome Assembly: assembles from short-reads

  • De Novo Bacterial Genome Assembly (Hybrid): assembles from a long-read and short-read file

For more details on the various assembly workflows and resulting analyses, check out this article!

Clicking "Run" on a single-input (short-read) assembly workflow will launch the assembly.

Clicking "Run" on a hybrid assembly workflow will provide you with a pop-up window in which:

  • You can choose to associate the assembly with an existing genome (which will set the new assembly as the preferred assembly for that genome), or create a new genome of the name you specify.

  • We will also ask you to select the second sample to include in the assembly, and to specify if this is a long- or short-read file. You can then launch your assembly.

Next Steps

Upon assembly completion, we automatically launch:

  • a corresponding QC analysis, which provides statistics on sequencing depth and coverage. It also estimates completeness and contamination, where possible

  • genome annotation

  • automated taxonomic assignment

We provide summaries of each in your Genome Library.

Learn more about what to expect for genome outputs here.

Reach out to us for pricing on the Genome Library and its associated features.

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