circlator

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Hi, I am using Rolling Circle Amplification technique which produces very long amplicons. After amplification, I fragment these products to approximately 1 genomelength and sequence this by MinION. I assembled...

severst

I run circlator with this command: circlator all --assembler canu --merge_min_id 85 --merge_breaklen 1000 --threads 24 final.genome.scf.fasta canu_correct/Kleb_canu_correct.correctedReads.fasta.gz circlator using Nanopore reads, our assembly was made on masurca using nanopore...

Frazapel

Hi, first of all, this is not an issue, instead it's a silly question about using it in a non-standard context. Here is my question: I have a virome metagenome,...

housw

canu 1.6 does not contain v. in its version

1

running circlator progcheck with canu 1.6 does not succeed, with the following error : Found canu but couldn't get version. the regex is "^Canu.*v.?([0-9][0-9\.]+)" and the canu -version command returns...

gerald2545

Hi, this warning is a bit vague. What do you think about making it say something like "output directory already exists, so quitting to avoid overwriting files." Or if there...

conchoecia

adding Racon assembly pipeline

1

Hi, Racon pipeline is very fast, compared to Canu and it would be great to have Racon as an option in circlator. ``` minimap2 -t 8 -x ava-pb \ input.fasta...

mictadlo

Racon assembly output with circlator

2

Hi, I ran a PacBio chloroplast assembly with Racon in the following way: ``` source activate minimap2 minimap2 -t 8 -x ava-pb \ input.fasta \ input.fasta | gzip -1 >...

mictadlo

I got the below error and I am not sure how to fix it: ``` WARNING: SPAdes version 3.11.1 is being used. It will work, but better results are usually...

mictadlo

use circlator to fix mitochondrial contig only from canu assembly

2

Can I apply circlator to the faulty Mt contig which is present as a partly self overlapping duplicated sequence resulting from assembling the circular chromosome? I have already assembled using...

splaisan

Hi, I'm running circulator all on hgap assembly to final circularize the contig but had an error during step3 with spades Here is the error log: === Stack Trace ===...

wenluo711