Brief instructions

Brief instructions

Although Circlator is modular, the most common way to use Circlator is to run the complete pipeline with a single command. Brief instructions for how to do this are given below.

Input files

Circlator requires corrected reads in FASTA or FASTQ format (which can be gzipped, or actually any format that BWA MEM will accept) and an assembly in FASTA format. Common long read assemblers output the required files, as listed here.

Output files

The pipeline is finished when the file 06.fixstart.ALL_FINISHED is written. The final output FASTA file of the new assembly is called 06.fixstart.fasta. All intermediate files from each stage of the pipeline are also kept in the output directory. If you want to know why Circlator did not circularize a contig that it should have, please read the troubleshooting section.

Circularization log files

The file outprefix.circularise.log summarizes whether or not, and why, each contig was circularized.

PacBio data

Given an assembly assembly.fasta in FASTA format and corrected PacBio reads in a file called reads, run

circlator all assembly.fasta reads output_directory

Use Canu instead of SPAdes

By default, SPAdes is used for reassemblies of contig ends. Canu can be used instead, which may give better results.

circlator all --assembler canu assembly.fasta reads output_directory

Nanopore data

Currently, nanopore data is of worse quality than PacBio. The parameters must be relaxed a little to use nanopore reads because the defaults assume PacBio data. Run it like this:

circlator all --merge_min_id 85 --merge_breaklen 1000 assembly.fasta reads output_directory

if you have corrected nanopore reads instead of corrected PacBio reads.

Contig merging

By default, Circlator will merge pairs of contigs, if there is an unambiguous join evident from the SPAdes reassembly of the reads. This stage can be disabled using the option --no_pair_merge, for example the PacBio example above would become:

circlator all --no_pair_merge assembly.fasta reads output_directory

Polishing

We recommend that the output assembly is polished using Quiver, or Nanopolish.