A standard file format defining the ordering and orienting of genome assembly sequences.

An assembly "patch" is a sequence that fills an existing or an implied assembly gap. Patches refer to one of the following sequences:

• A sequence that fills an assembly gap
• A sequence that continuously joins distinct assembly contigs

Genome assembly sequences ordered and oriented with gaps between them.

This describes query assembly sequences that are not used to build longer sequences.

There are many ways to define if alignments are "unique". RagTag uses the concept of "unique anchor filtering" first introduced by Nattestad and Schatz, 2016. Each bp in an alignment is unique if it does not overlap any other alignments with respect to the query sequence. Alignments are either entirely composed of unique or non-unique bp, or they have both unique (anchor) and non-unique bp.