Home
Long-read sequencing and assembly have come a long way in recent years. 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! Common problems include:
- Failing to circularise sequences, either duplicating or omitting sequence at the start/end of a contig.
- Producing spurious contigs, e.g. assembling a repetitive part of the chromosome into a separate contig.
- Omitting entire replicons, e.g. failing to include a small plasmid.
- Creating medium-scale indel errors, e.g. deleting 50 bp from the genome.
- Creating 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 problems listed above?
Autocycler addresses these issues by combining multiple alternative assemblies of the same genome (e.g. from different assemblers or different read subsets) into a high-confidence consensus assembly. It achieves this by compressing input assemblies into a compacted De Bruijn graph, clustering similar sequences, trimming overlaps and resolving ambiguities. The result is a long-read assembly you can trust!
Autocycler is designed to be both fully automated and human-guided. This means that unlike its predecessor Trycycler, Autocycler can be run without any human intervention, allowing it to be used on large numbers of genomes. But it still allows for manual examination and intervention when desired.
If you’re new to Autocycler, follow these steps to get started:
- Install Autocycler: see the Software requirements and installation page.
- Learn the basics: check out the Illustrated pipeline overview and quick start pages.
- Try the demo: practise using Autocycler on the provided demo dataset.
Happy assembling!