4. Reference Creation

Overview

EPITOME creates references from a set of input sequences that have passed the initial QC filters. Below is a descript of each step of the reference creation process.

Sequence Clustering

The first step of reference creation is to split quality filtered sequences into closely related clusters (controlled using --dist_threshold). This is accomplished using a multi-step process, which was designed to handle very large data sets. A general overview of this process is described below:

1. Hierarchal clustering

• A subset of sequences are randomly selected (controlled using --max_cluster).
• The subset is split into clusters using the "complete linkage" of pairwise average nucleotide identity (ANI) between sequences (controlled using --dist_threshold).

2. Assign clusters

• Representatives of each cluster are selected.
• Remaining sequences are assigned to one of the clusters by comparing to the representatives using the pairwise ANI.
• Unassigned sequences are passed to step 1.

This process is repeated until all sequences have been assigned into a cluster.

Note

Average nucleotide identity is estimated using sourmash.

Consensus Generation

Condensing References