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 go back to the assembly stage and see if better assemblies can be generated as Trycycler input. It might be necessary to resequence the genome, getting longer/deeper/better reads to work with.
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.