Why didn't my assembly go well?

There are two common reasons for Autocycler to fail to produce a completely resolved assembly:

1. The input assemblies were low quality.
2. The genome contains one or more linear sequences.

Low quality input assemblies

Linear sequences

Autocycler can struggle to fully resolve linear sequences for a few reasons:

• Input contigs can extend past hairpin ends, leading to erratic contig lengths. The Autocycler trim step can often but not always repair this.
• Input contigs can be inconsistent regarding where blunt ends terminate, leading to unresolved sequences in the Autocycler resolve step.

See the Linear sequences page for a more thorough description of these problems. Future versions of Autocycler will aim to improve behaviour on linear sequences.