circlator
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sanger-pathogens
A tool to circularize genome assemblies
Hi, I'd like to use circlator to assembly a mitochondrion genome. I have (PacBio) reads and "linear" contig-level assemblies for a number of samples, as well as a different "reference"...
Dear Circlator Team, thanks for this great tool. I have one question: I am using Circlator to circularise mitochondrial assemblies, so far so good. I then want to set the...
Hi, I am getting following error: Traceback (most recent call last): File "/home/anaconda3/envs/bioinfo/bin/circlator", line 58, in exec('circlator.tasks.' + task + '.run()') File "", line 1, in File "/home/anaconda3/envs/bioinfo/lib/python3.7/site-packages/circlator/tasks/all.py", line 74,...
If someone using circlator 1.5.5 and canu 2.2 encounters the error: 'Found canu but couldn't get version' The fix is to change the following line in `external_progs.py`: ``` 'canu': ('-version',...
Hello, I am trying to run circlator using canu (v 1.9)as the assembler circlator all --assembler canu ~/Desktop/CANU/KU15176/assembly/KU15176.contigs.fasta ~/Desktop/CANU/KU15176/corrected_KU15176/KU15176.correctedReads.fasta.gz ~/Desktop/Circulator_KU15176CANU however the run gets terminated and I am getting the...
hi @andrewjpage and team i encountered the following error with one of my samples (works fine on the other samples): `The reason why should be in the spades.log file in...
When I run circlator ```circlator test_output```, I get error messages at the merge step. It seems to be a problem with running nucmer: ```Running Circlator on test data... Made output...
In a number of cases, circlator appears to run forever. It's spades-bwa that's doing it. Has anyone else noticed this? Is that a reason to run SPAdes 3.7? I tried...
I have Illumina reads for isolates from an evolution experiment but only have nanopore reads for the ancestral strain. It looks like the main differences between the evolved strains and...
