Glossary

anchor: a unitig which appears exactly once in of the cluster's contigs. In the 3_bridged.gfa graph, these are coloured green.

bridge: a connection between two anchor unitigs. In the 3_bridged.gfa graph, these are coloured pink.

conflicting bridge: a bridge which conflicts with other bridges. All conflicting bridges cannot be applied to a unitig graph (applying one will prevent the application of another), so the least-supported conflicting bridges will be discarded.

consentig: a consensus sequences produced by merging anchors and bridges. Can be found in the 4_merged.gfa and 5_final.gfa graphs made by Autocycler resolve. In the 4_merged.gfa and 5_final.gfa graphs, these are coloured blue.

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).

open end: the end of a linear sequence without a hairpin structure.

tig: a catch-all term for all of the words which end in 'tig'.

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 compacted De Bruijn graphs: input_assemblies.gfa (made by Autocycler compress), 1_untrimmed.gfa (made by Autocycler cluster) and 2_trimmed.gfa (made by Autocycler trim).

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