An Alignment is an analysis providing sensitive local alignment of a WGS samples against a specific reference genome sample. It has the same properties as an analyses, but lacks the analysis_type field and also includes a tax_id field indicating what .

At this time, there are no v1 API routes for accessing the alignment statistics (e.g., percent identity, coverage, and depth), but alignments can be viewed on the One Codex platform directly. Here's an example public alignment and a list of all alignments for that sample:

Property

Description

$uri
string

The analysis/alignment ID encoded as an addressable URI

created_at
date-time

Timestamp for when the analysis was created on the One Codex platform, encoded as a RFC 3339 timestamp

complete
boolean

If the alignment is complete. Incomplete or pending analyses will show a icon in the One Codex web application.

success
boolean

true if the alignment was successful.

error_msg
string

An error message if the alignment failed. Should generally be "" or null if the analysis succeeded or is pending.

job
string

A reference to the versioned job underlying the alignment, e.g., {"$ref": "/api/v1/jobs/d512cb556241440f"}.

sample
string

A reference to the sample underlying the alignment, e.g., {"$ref": "/api/v1/sample/0ee172af60e84f61"}

tax_id
string

The taxonomy ID used in determining which reference to align against. Taxonomy IDs are NCBI IDs encoded as strings, and may be species or sub-species level. Alignments will use the best available reference genome available.