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Hi,
I have just started to assemble bacterial strains from my first MinION run. In the polishing step I get the error OSError: [Errno 26] Text file busy: '/media/sf_BioLinux-vymena_dat/Run1_part_da…
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I have got an 40 threads CPU and 126 GB ram in my computer with Ubuntu 18.04. I installed the canu 1.8 with brew from homebrew/bio. I generated the FASTQ file from BAM files with bam2fastx 1.3. I used…
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Hi,
If you are interested in more competition, you might want to add my [pfasta](https://github.com/kloetzl/pfasta) parser to your benchmarks. It doesn't do FASTQ, but prints nice error messages. :…
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Hi, I am running canu on my raw nanopore reads generated through MinION.
Here is the command I am running:
```
canu --assemble -p pb3 -d pb3-ont corOutCoverage=500 \
corMinCoverage=0 corMhapSens…
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I am research support helping a researcher run canu so apologies because I am not familar with the full context of this issue.
We are running on a slurm cluster (Linux 4.4.0-164-generic x86_64)
…
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Hi Kamil,
I am using smudgeplot to look at the state of ploidy in a plant pathogenic fungs. I counted kmer coverages with KMC and then plotted with smudgeplot as instrected in the tutorial. The fung…
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**planning**
before new year
- in memory index to speed up Unipept database construction from Uniprot + NCBI Taxonomy
- use new indexing in Unipept database construction scripts
- ship rails platform…
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Hi there!
I've been working on the assembly of a highly repetitive plant genome for a while. The command I'm using is:
nice -2 nohup /ohta/joanna.rifkin/canu/Linux-amd64/bin/canu -p Rumex -d Ne…
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Hi,
I am trying to run Canu timing in a local computer. I installed canu following the instruction in GitHub:
```
git clone https://github.com/marbl/canu.git
cd canu/src
make -j
```
I i…
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I'm using canu 1.8 on a galaxy service
Command:
```
canu -p canu -d out_dir genomeSize=5m rawErrorRate=0.5 correctedErrorRate=0.144 minReadLength=1000 minOverlapLength=500 corOutCoverage=40 con…