Assemblage is a nextflow pipeline used for generating assemblies. Documentation can be found here. The pipeline is currently under construction, but the plan is to generate the following tracks:
This track generates assemblies using the normal Illumina paired-end reads.
Status: Complete
This track generates assemblies based on both Illumina and Nanopore reads, using hybrid assembly.
Status: Under construction
This track is using the long-read-first assembly method, compares that to a hybrid assembly, and merges all plasmid sequences by the use of trycycler.
Status: Not yet started