Bad dataset analysis
To begin, I ran Trycycler cluster on the assemblies:
trycycler cluster --reads reads.fastq.gz --assemblies assemblies/*.fasta --out_dir trycyclerWhich produced this output.
A whopping 69 clusters were made, and the tree looks hideous:
There are no clear clusters here on which we can apply further stages of Trycycler 😢
This dataset was a bit of a trick – it's unusable rubbish. In a situation like this, it is necessary to back up to an earlier stage. Perhaps different assemblers or assembly parameters can make better input assemblies for Trycycler. Or it might be necessary to resequence the genome to get longer/deeper/better reads to assemble.
It's worth reiterating here: Trycycler is not a tool for coaxing a difficult read set into a decent assembly. Rather, it's a tool for taking a good read set and making a great assembly.