Questions tagged [canu]

The long-read genome assembler suitable for long reads having a relatively high error rate, such as PacBio and Nanopore data.

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Optimum parameters for genome assembly via canu

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 ...
menten's user avatar
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3 votes
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Can the canu assembler output a fastq file of the final assembly just like HGAP4?

I have assembled some genome from Sequel PacBio data both with HGAP4 on the SMRT Link interface and using canu on the command line. The HGAP4 assembler outputs a fastq file of the final assembly such ...
Biomagician's user avatar
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7 votes
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Canu assembly not making a single consensus?

I've downloaded reads from this BioProject. Using canu with default parameters (no correction), I've got 4 contigs, none of which really look like the reference plasmid here. The command I used was: ...
thestatnoob's user avatar
3 votes
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How to submit a canu job on LSF high-performance computing cluster farm?

I am currently running canu on an LSF Linux server using the following script called ...
Biomagician's user avatar
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4 votes
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Error rate setting in Canu error correction

I want to use Canu to correct my nanopore long read (version: MinION R9.5), but I am not quite sure how to set the correctErrorRate. Should I follow the Canu manual (Nanopore R7 2D and Nanopore R9 1D ...
raymond's user avatar
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18 votes
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How can I improve a long-read assembly with a repetitive genome?

I'm currently trying to assembly a genome from a rodent parasite, Nippostrongylus brasiliensis. This genome does have an existing reference genome, but it is highly fragmented. Here are some ...
gringer's user avatar
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