cizydorczyk
cizydorczyk
Hello, I noticed recently that when I assemble a genome with Shovill and then use Snippy to call SNPs against that genome using the same reads as used to assemble...
Hello, I'm having some trouble understanding the tree scale that is output in the newick formatted tree by Gubbins. Specifically, branch lengths in this tree are on the order of...
Just wondering if there are any plans to implement logistic mixed models (in addition to existing linear models) for association testing? As the documentation mentions, using a linear model with...
When I look at the plastic_regions.tsv file, the number of genes in each RGP for each isolate is reported. Summing provides the total number of genes in RGPs for a...
When I try to run chewbbaca createschema, I get the following error: ``` $ chewBBACA.py CreateSchema -i enterobacter-assembly-copies/ -o ./ecloacae-schema --n ecloacae-wgmlst-schema --ptf GCF_001875655.1.trn --cpu 24 chewBBACA version: 3.3.3 Authors:...
Is there an option to output the coordinates of an insertion or deletion in the query sequence? For example, if I wanted to investigate the genes present in a 5kb...
Hello, I am trying to run DAPC cross-validation using the xvalDapc() function. The data set I am working with is a matrix of 155 rows and ~98K columns representing SNP...
Hello, When I run the dapc() function on a SNP dataset of ~ 100k SNPs split into 31 clusters, at the stage where I get asked how many discriminant functions...
Hello, Let me start off by saying the tool looks great! I've had a major problem dealing with incomplete/mis-annotated/truncated genes in pangenome analyses, and no other tools have been designed...
I am interested in assembling some draft bacterial genomes using a complete genome as a reference to guide the assembly process. While I expect some minor differences, most of these...