Stephane Plaisance

Similar question, can we polish a chloroplast using racon and minipolish? Although eukaryote it is ciscular and is of prokaryote origin but it also has repeated regions which I suspect...

Hi! I have today the same error with or without --bam-fix, --rg-id and --rg-sm all set. Is there an update and fix to have ngmlr work with the current samtools?...

Hi Jon, I am still learning your tool and really start to enjoy it, thanks for that great resource! I still have the message ```Fontconfig error: No writable cache directories```...

I have create a function to do it based on what I found in circlize doc and the vis_circos buitl-in (not very documented!) _I am not able to submit this...

same here ``` The following command failed with exit code 1 canu -useGrid=false gnuplotTested=true -assemble genomeSize=0.1m -d /data2/gridion_data/2741/circlator_ont_canu-out/03.assemble -p canu -nanopore-corrected /data2/gridion_data/2741/circlator_ont_canu-out/02.bam2reads.fasta ERROR: Parameter 'gnuplotTested' is not known. ```

Should I collect by mapping only the reads contributing to the MT chromosome contig and use them in the circlator pipeline or take all the reads of the project (incl...

I second this and would love that the pull request be processed please developers!

Thanks, I hope the developers will implement this at some point.

> That's after I excluded hypotheticals. BUT It turns out that those stats are all wrong, and include lots of chromosomes. WHY? https://ftp.ncbi.nlm.nih.gov/refseq/release/plasmid/ has all the CDS of chromosomes in...

thanks @sorenwacker > ``` > mamba create -y -c anaconda -c bioconda prokka pandas seaborn ipykernel perl-bioperl==1.7.2 -n prokka > ``` this worked for me on a ubuntu 18 machine...