Main tool : trycycler
The container also contains :
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.