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Genome Assembly Workflows
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 assemble and store their private genomes.

We've spent a lot of time over the last few years building high quality genome assembly pipelines for various organism types. These pipelines have been used by some of the largest microbial cell culture collections, and now we bring them to you.

Assembly Workflows

Genome assembly is currently available for various sequencing technologies for bacterial and archaeal genomes. We're working to expand our pipelines to other taxa. Keep an eye out for updates in the coming months!

Each assembly workflow includes quality assessment of reads prior to assembling with a superkingdom-specific assembler. 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 available.

  • genome annotation

  • automated taxonomic assignment

We provide summaries of each in your Genome Library.

Below, you'll find the main tool utilized for each step in the workflow.

Superkingdom

Sequencing Platform

Assembly Pipeline

Annotation Pipeline

Assembly QC

Bacteria / Archaea

Illumina

Shovill

Prokka

CheckM + Contig Stats

Bacteria / Archaea

Illumina + ONT

Unicycler

Prokka

CheckM + Contig Stats

Bacteria / Archaea

Illumina + PacBio

Unicycler

Prokka

CheckM + Contig Stats

Next Steps

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

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