Quick start

In brief, the steps involved in getting a Trycycler consensus assembly are:

• Prepare the input files:
  • Create multiple independent assemblies of the same isolate from a long-read set. Save these as assemblies/*.fasta.
  • Save the long reads used to generate those assemblies as reads.fastq (gzipped reads also work).
• Run Trycycler cluster to group similar contigs together:
  • trycycler cluster --assemblies assemblies/*.fasta --reads reads.fastq --out_dir trycycler
• Manually inspect the clusters to decide which are valid:
  • For this example, we'll assume cluster_001, cluster_002 and cluster_003 are the good clusters which represent replicons for which we want a consensus.
  • Delete or rename all other cluster directories (so you can glob for the good clusters with trycycler/cluster_*).
• Run Trycycler reconcile on each of the clusters:
  • trycycler reconcile --reads reads.fastq --cluster_dir trycycler/cluster_001
  • trycycler reconcile --reads reads.fastq --cluster_dir trycycler/cluster_002
  • trycycler reconcile --reads reads.fastq --cluster_dir trycycler/cluster_003
  • In order for these commands to complete, it may be necessary to delete or repair some of the cluster sequences.
• Run Trycycler MSA on each of the clusters:
  • trycycler msa --cluster_dir trycycler/cluster_001
  • trycycler msa --cluster_dir trycycler/cluster_002
  • trycycler msa --cluster_dir trycycler/cluster_003
• Run Trycycler partition to divide up the reads:
  • trycycler partition --reads reads.fastq --cluster_dirs trycycler/cluster_*
• Run Trycycler consensus to make a consensus sequence for each contig cluster:
  • trycycler consensus --cluster_dir trycycler/cluster_001
  • trycycler consensus --cluster_dir trycycler/cluster_002
  • trycycler consensus --cluster_dir trycycler/cluster_003
• Combine all consensus sequences into a single FASTA:
  • cat trycycler/cluster_*/7_final_consensus.fasta > trycycler/consensus.fasta

For more information, please look at the wiki pages for each of the steps involved.

If you're new to Trycycler, I'd recommend trying it out on the Demo datasets.