dutchscientist
dutchscientist
Currently all genomes are downloaded as cryptic filenames, such as: "GCF_000469325.1.fna" De FASTA header of that file is: "NZ_KI271582.1 Lactobacillus shenzhenensis LY-73 genomic scaffold LY73.Scaffold1, whole genome shotgun sequence" Is...
Is it possible to only download plasmids? NCBI Genome has a plasmid-specific page, but I don't see that option in ncbi-genome-download. Don't know how easy this is?
Often we have a (prokka-generated) Genbank file, but only want to use a small subsection of it in Clinker. I don't know how easy it would be, but could an...
Just noticed that the default depth has changed to 150x, but in the descriptor it still says 100x. Is there a specific reason for the increase?
First-world problem, I know. The latest version has "sw=shovill-spades/1.0.4" in the FASTA header, and the hyphen in that header makes programs like ParSNP from the Harvest suite that the genome...
When I try to install Roary 3.13.0 in a Conda (Mamba) environment, it works fine when the environment is set at python 3.7, but not in a 3.10 environment (the...
In more and more bacteria, there are enough MLST data to use the Clonal Complexes rather than the specific sequence type. For instance, the Campylobacter and Listeria files provided include...
I always use the " -r ! " switch to choose the reference sequence. In version 1.2 that works great, but version 1.5.6 duplicates the chosen reference in the tree,...
I am using sqm_mapper.pl to clean up samples from host sequences, in the current case a combined human and pig genome. That works great, but every time I start a...
I am running a lot of samples with 1.65post1 (3 virtual machines parallel with 22 cores and 70 GB RAM), and due to a human error I needed to run...