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One Codex Alignments

An Introduction to One Codex Alignments, and How to Run Them

Denise Lynch avatar
Written by Denise Lynch
Updated over a week ago

Intro to alignments:

One Codex is excited to share our alignments job for samples. The alignments pipeline is a natural extension of our classification analysis, as once an organism is shown as present in a sample, it’s often important to view how reads in the sample match the genomes identified.

Uses for One Codex alignments:

There are many uses for alignments, we’ve highlighted a few below.

Determining depth, coverage, and identity:

These three metrics are key to determining support for organism presence in a sample. Depth shows you the average read coverage per nucleotide of the reference, Coverage; the number of the reference nucleotides covered, and Identity; the proportion of exactly mapping bases over the total mapping bases.

Insert size calculations:

Paired-end reads need to be aligned to calculate sequencing metrics such as insert size for inserts longer than the paired sequencing length. In our summary, we provide the relevant insert sizes for the alignment.

Mapping genomic reads:

When troubleshooting a classification, mapping and viewing coverage plots can be useful for manually determining just how much of a given reference is present in the sequencing run of interest. They are also useful in determining regions of divergence between the reference and the studied sample.

Running an alignment job

An alignment job can be started like other One Codex analyses, either on the sample page of the sample you wish to test, or by searching for the sample on the run analysis page.

The difference between starting the assembly job and other One Codex analyses is with assemblies you will first need to search for a genome to align to on the jobs page. These can be searched for based on the species' name. If the reference is present for genome, it will show up in the autocomplete. Select one or more genomes to align to and select run.

Multiple alignments can be run on the same sample, all alignments will be viewable in the alignments on the sample page.

Accessing your alignment:

Once the alignment is complete you will be able to access the results by selecting alignments on the sample page.

This will bring you to the alignments tab. Here you will find a brief overview of all the alignments completed.

Selecting View Alignment will show more details of the alignment including insert size metrics, a detailed coverage plot, as well as an interactive IGV window.

A link to an example alignment can be found here: Link

Bioinformatics Details the One Codex Alignment Analysis

The One Codex alignment pipeline returns a report detailing the multiple sequence alignment results for a query sequence file mapped to a reference assembly. Primary alignment of reads leverages Minimap2.

After the sequence alignment is complete, we calculate alignment metrics of coverage (the fraction of the reference covered by at least one read), depth (the mean sequencing depth across the entire reference), and identity (the cumulative sequence identity) these appear in the alignments tab of the report. We also calculate insert metrics for reads in the alignment. These are shown when navigating to view each alignment.

Let us know if you have questions about the One Codex alignments assay, we are always available at

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