RvV1979

In order to reduce clutter I wish to show labels for selected genes only. To this end, I created /note tags only for those genes and set gene label type...

Sometimes, it is useful to be able to differentiate between different clades or orthologous groups within a tandem array of homologous genes. See the example below, where a tandem array...

Currently, colors indicating cluster groups represent a rainbow gradient across the loci. Consequently, when analyzing large gene clusters, neighboring genes have very similar colors. This can make it difficult to...

It seems clinker does not work as intended when multi-exon genes are annotated with separate CDS instead of with join(). When this is the case, CDS exons are considered separately...

I wish to apply this workflow to a non-model plant genome for which no reference is readily available at the snpEff database. Is there a way to direct snpEff to...

Is it possible to standardize SSC orientation?

3

In the [wiki](https://github.com/Kinggerm/GetOrganelle/wiki/FAQ#what-are-the-differences-of-complete1path_sequencefasta-and-complete2path_sequencefasta-output-files) you write: "You can pick the configuration of which the SSC region is in the same direction with most of your data or outgroup, which makes downstream...

number of threads in bwa mem wrapper

2

Hi, apologies for this very basic question but I am wondering how snakemake deals with the threads parameter in the bwa mem wrapper. The wrapper uses this parameter to specify...

using ensemblgenomes for non-vertebrate references

2

Hi Johannes, I am trying to implement the https://github.com/snakemake-workflows/dna-seq-gatk-variant-calling workflow for non-vertebrate (plant) genomes that are available through ensemblgenomes.org. However, the https://github.com/snakemake/snakemake-wrappers/tree/master/bio/reference wrappers use only the canonical ensembl ftp site....

Thanks for developing such a versatile tool; especially the ability to integrate annotations is very nice. However, I find that running comparisons of relatively long sequences is prohibitive. Specifically, I...

AlignK not aligning clusters across k

2

I am having trouble aligning K based on my slist (attached in RDS format here: (https://github.com/royfrancis/pophelper/files/12670714/slist.RDS.zip) ) my code ``` slist