I have been trying to assemble my genome via canu. Canu gave me about 200 contigs using default parameters. My genomesize is ~9Mbp. Can you recommend some parameters I can tweak to decrease the contigs number?
The canu parameter reference guide is always a good place to start.
It would help to know a little bit more about what your assembly looks like. E.g.
- what is your n50, n90...?
- What is your dataset coverage?
- Have you run any tools like quast to evaluate quality?
- What is your input data type (probably PacBio)? Read length distribution?
- What is your expected chromosome/replicon number?
- Have you compared the assembly to any other data, e.g. genomes of close relatives? (quast can do this)
Basically, why do you think that 200 contigs is too many contigs? Sometimes you just don't have enough coverage to get more contiguous/"nice" assemblies. That's not to say it's not possible, of course, just that we don't have enough information to evaluate.
It's possible that some of those contigs are small and artefactual, so you might get rid of them with just length/coverage filtering. You can do some of this in canu itself (see "Output Filtering" section).