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7 votes
Accepted

How can I improve a long-read assembly with a repetitive genome?

"A few" 100kb reads won't help much. You need to apply the ultra-long protocol, which is different from the standard protocol. You can't resolve 20kb near identical repeats/segdups with 10kb ...
user172818's user avatar
  • 6,535
3 votes

Error rate setting in Canu error correction

It's generally a good idea to trust the "official" suggestions. You can also adjust the error rate based on coverage according to parameter reference: For low coverage datasets (less than 30X), we ...
burger's user avatar
  • 2,199
3 votes

Canu assembly not making a single consensus?

Looking that the link you provided only 30% of the reads appear to be e. coli. I would suggest filtering the reads for those that align to e. coli and see where that gets you. Did the original ...
Bioathlete's user avatar
  • 2,574
2 votes
Accepted

Can the canu assembler output a fastq file of the final assembly just like HGAP4?

I've created an issue on the Canu github repository for this. I'm not aware of any existing functionality to output FASTQ files, but think that this would be a useful feature to have. It would be ...
gringer's user avatar
  • 14.2k
1 vote

Optimum parameters for genome assembly via canu

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 ...
Maximilian Press's user avatar
1 vote

Canu assembly not making a single consensus?

The E. coli genome is closer to 4.6 Mb in size; if there are a large quantity of host reads in there, then they'll take over the reads and there won't be enough for your target plasmid. By default, it ...
gringer's user avatar
  • 14.2k
1 vote

How to submit a canu job on LSF high-performance computing cluster farm?

I haven't used canu for several years but looking back at my labbook I ran it with two additional flags: -minThreads=8 -maxThreads=8 My memory on the subject is a ...
Graeme's user avatar
  • 181

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