Main tool: trycycler

Additional tools:

• miniasm 0.3-r179
• minimap2 2.24-r1122
• muscle 3.8.1551 (recommended version)
• mash 2.3
• R package 'ape' 5.7
• R package 'phangorn' 2.11.1

Trycycler "tries" different assemblies to find the one most supported by long reads.

trycycler subsample --reads reads.fastq --out_dir read_subsets

trycycler cluster --assemblies assemblies/*.fasta --reads reads.fastq --out_dir trycycler

trycycler reconcile --reads reads.fastq --cluster_dir trycycler/cluster_001

trycycler consensus --cluster_dir trycycler/cluster_001

It is highly recommended to read Trycycler's wiki for full usability and reasoning.