FAQ and miscellaneous tips

How does Autocycler compare to Trycycler?

Autocycler was designed to be a faster and automated successor to Trycycler. Both tools perform the same task: combining multiple alternative assemblies of the same genome into a clean consensus assembly.

• Trycycler was designed to be human-guided.
• Autocycler was designed to be automated (but still allow for human intervention).
• They should give very similar results, but Autocycler is probably easier to use.
• Performance:
  • Trycycler is slower. Written in Python, and it has a few steps which involve aligning all the reads, which is slow.
  • Autocycler is faster. Written in Rust and doesn't align reads.

Most users will probably be better off with Autocycler!

Can Autocycler be used on eukaryote genomes?

For Autocycler to work, the input assemblies need to mostly be complete: one sequence per piece of DNA in the genome. So if T2T assemblies are possible, then Autocycler should work!

However, phased diploid assemblies might create a problem in the clustering step. If there is a lot of heterozygosity, the two haplotypes for each chromosome might separate in the UPGMA tree, in which case clustering might work (potentially requiring manual specification of the clusters). But more likely it will require the user to separate the haplotypes in the input assemblies. I.e. split each phased input assembly into a maternal assembly and paternal assembly, then run Autocycler twice (once for maternal, once for paternal).