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The problem

Long-read assembly has come a long way in recent years, and there are many good assemblers available. Since bacterial genomes are relatively simple (not too large and not too many repeats), a completed assembly (one contig per replicon) is often possible when assembling long reads.

But even the best assemblers are not perfect! They often fail to circularise sequences, either duplicating or omitting sequence at the start/end of a contig. They sometimes produce spurious contigs, e.g. assembling a repetitive part of the chromosome into a separate contig. They sometimes omit entire replicons, e.g. failing to include a plasmid. They sometimes create medium-scale indel errors, e.g. deleting 50 bp from the genome. And they occasionally create large-scale misassemblies, e.g. a significant structural rearrangement.

So imagine that you've done long-read sequencing of a bacterial isolate and assembled the reads. The result looks like a nice completed assembly (e.g. a big circular contig for the chromosome and a couple of smaller circular contigs for plasmids), but how can you be sure that it's free from the kinds of problems listed above?

The solution

Autocycler is a tool that takes as input multiple separate long-read assemblies of the same genome (e.g. from different assemblers or different read subsets) and produces a consensus long-read assembly that you can trust!

An important caveat

Autocycler does not ensure a perfect assembly of the underlying genome, because systematic basecalling errors can create small-scale sequence errors. Incorrect homopolymer lengths are a common example of this problem, e.g. AAAAAAAA becoming AAAAAAA.

But if all goes well when running Autocycler, small-scale errors will be the only type of error in its consensus long-read assembly. You can then polish your Autocycler assembly to repair these small-scale errors, e.g. long-read polishing with Medaka then short-read polishing with Polypolish and Pypolca. An Autocycler+Medaka+Polypolish approach to assembly can therefore yield the best possible bacterial genome: Autocycler fixes the medium-to-large-scale errors while polishing fixes the small-scale errors.

Where to begin?

Are you new to Autocycler and interested in trying it out? If so, you'll first need to get it installed, so check out the Software requirements and installation page.

After that, I'd recommend that you look at the Illustrated pipeline overview and read the quick start pages. Autocycler can be run in a fully automated manner or with manual intervention.

Finally, I'd suggest that you practise using Autocycler on the provided demo dataset. Happy assembling!