Minimus2 circularization pipeline

Methods

Circlator comes with an option to circularize contigs using this protocol from PacBio using minimus2. However, the Circlator version has a couple of modifications intended to improve the results. This protocol is completely independent of the main Circlator circularization pipeline, and is included for convenience because the protocol involves several manual steps.

1. By default, before attempting to circularize any contigs, minimus2 is run on the input contigs with the aim of merging any overlapping contigs. This is not in the above protocol, and can be skipped.

2. An attempt is made to circularize each contig individually, instead of in one run with all the contigs. Each contig is broken at its middle, to make two new contigs. These two contigs are input to minimus2. If minimus2 outputs a single contig, then that contig is kept and the two pieces are not used. Otherwise, the original contig (before being broken into two) is kept.

3. We have found that minimus2 often crashes. When this happens, our implementation of the protocol simply keeps the original contig and moves on to the next contig to be circularized. This means that contigs are circularized whenever possible and it is not necesary for minimus2 to successfully run on all contigs to produce a result.

4. It is up to the user to run Quiver after running the circularization.

How to run

It is assumed that toAmos and minimus2 are in the user's path, which in reality means that AMOS must be installed.

Run the protocol with:

circlator minimus2 input_assembly.fasta prefix_of_output_files

To skip the initial merging stage, use

circlator minimus2 --no_pre_merge input_assembly.fasta prefix_of_output_files

The final output file is called

prefix_of_output_files.circularise.fasta

and a log file with basic information of what happened is called

prefix_of_output_files.log