Glossary

anchor unitig: a unitig which appears exactly once in of the cluster's contigs.

bridge: a connection between two anchor unitigs.

conflicting bridge: a bridge which conflicts with other bridges. All conflicting bridges cannot be applied to a unitig graph, i.e. applying one will prevent the application of another.

contig: a sequence from one of the input assemblies. Even though different assemblers might use different terms for their assembled sequences, in the context of Autocycler, I refer to them all as 'contigs'. This is to distinguish input assembly sequences (contigs) from Autocycler's sequences (unitigs).

unique bridge: a bridge which doesn't conflict with any other bridges. All unique bridges can be applied to a unitig graph.

unitig: a sequence in one of Autocycler's graphs. Generally, the term 'unitig' refers to a high-confidence sequence consistent with most/all of the data, and this matches up well with the sequences in the initial compacted De Bruijn graph created by Autocycler compress. However, I continue to use the term 'unitig' for sequences in later-stage graphs as well (such as those made by Autocycler trim and Autocycler resolve). This is to distinguish input assembly sequences (contigs) from Autocycler's sequences (unitigs).

unitig graph: another name for Autocycler's compacted De Bruijn graph or the downstream graphs derived from it.