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) 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.

PacBio data

Given an assembly assembly.fasta in FASTA format and corrected PacBio reads reads.fastq in FASTQ format, run

circlator all assembly.fasta reads.fastq 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.fastq output_directory

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

Polishing

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