How to assess an Autocycler assembly
How do you know if your Autocycler assembly went well or not? This page offers a few approaches.
The Autocycler combine command produces a final assembly by combining all of the clusters. Hopefully, each cluster resolved to a single consentig, in which case it will print this at the end of its stderr output:
Consensus assembly is fully resolved 😄
If, however, one or more clusters did not resolve to a single sequence, you'll see this message instead:
One or more clusters failed to fully resolve 😟
If you load the consensus_assembly.gfa file in Bandage, you will hopefully see something like this. Note that each component of the graph has only one sequence, and each sequence is coloured blue, indicating that it's an Autocycler consentig. |
However, if things didn't go as well, you might see something like this. Note that one component of the graph has multiple sequences where non-consentigs are coloured orange. |
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The Metrics page describes all of the assembly metrics generated by Autocycler, but for assessment purposes, the most useful is likely the consensus_assembly_fully_resolved metric, which can be true or false. You can find this metric in the consensus_assembly.yaml file made by Autocycler combine in your Autocycler output directory.
Alternatively, you can use Autocycler table to access the metrics (including consensus_assembly_fully_resolved). If you only have one Autocycler assembly to assess, these commands will build a simple one-row TSV with some key metrics:
autocycler table > metrics.tsv
autocycler table -a autocycler_out >> metrics.tsv