How to run Trycycler

Running Trycycler is a multi-step process involving five separate Trycycler commands. It's not all automated into a single command because there are some judgement calls and/or human interventions to be done between the steps.

For a brief overview, check out the Quick start page. For more detail:

• Step 1: Generating assemblies
• Step 2: Clustering contigs
• Step 3: Reconciling contigs
• Step 4: Multiple sequence alignment
• Step 5: Partitioning reads
• Step 6: Generating a consensus
• Step 7: Polishing after Trycycler