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@gokeson Could you provide advice on how the pipeline should handle plasmids? In a test run I detected a 7.5kb plasmid, full length!
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# What we want
Allow SYC to browse the Resources in eLab (such as plasmids, or primers, or dna sequences...).
# How it could be done
1. User selects "eLabFTW" as a source (similar to Addgene/…
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Consider the attached FASTA file. It contains two sequences that match a plasmid from RefSeq at 99% IDY. However, there are classified as virus by viralVerify. Looks strange.
[ic5-metaplasmidspades.p…
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Hi,
I am trying to run deeplasmid on the HPC at my workplace. The computer support team have installed the software. We have been trying it out and came across this error where it cannot find the …
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Hub plasmids get marked with a black star in the visualisation, and there's a toggle button that removes them, but any hub plasmids found in later iterations are black circles and don't get removed in…
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Hello,
I'm using PHEnix for an organism where the reference genome has plasmids.
I want to leave the plasmids in for the mapping and snp calling so that plasmid reads don't map to the chromosome…
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First, thanks so much for this fantastic tool
I was analyzing a collection of plasmids from pseudomonads, and came across predictions of relaxases that were unexpected, because I got a prediction w…
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Hi,
I'm looking to tune the parameters for wtdbg2 (or troubleshooting in general) for recovering a smaller plasmid (~5k in size, many reads with the entire plasmid contained) that miniasm finds, bu…
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Hi!
I am grying out this tool now. I installed via conda, and am using it on a slurm run cluster with srun. Have asked for 10 cpus. I have a file list containing 8 plasmid fasta seqs. The plasmids …
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Hi @gbouras13 ,
I use hybracter to assemble bacterial genomes and plasmids from long read sequencing. I want to assemble single plasmids from long read sequencing but hybracter does not work with o…