jrober84

So I dug into this a bit more and the issue seems to be that snippy-core skips processing sequences as soon as it encounters 1 sequence which has an ambiguous...

I occasionally get this issue but it is usually the conda environment itself. I usually find the easiest way to solve it is with a new conda environment. You can...

Version 3.1.0 will implement this update, thank you for pointing this out!

So the reason for the fixing of fasta headers is that spaces and other characters can cause issues with tools like blast but there are a variety of tools that...

The issue #87 shows the problem with super long headers. I have made a change to the code that all sequences will be renamed in the format {int}_{md5}_circular={status} for all...

I will label this one as an enhancement for future versions. The clusters.txt file in the databases/ directory contains the typing information for all of the plasmids in the reference...

I am thinking to create a series of single-linkage flat clusters based on mash distances, between your input and the reference database and provide basic summary statistics on the average...

Hello, please try installing using conda as there are other external programs you will need to have installed as well. % conda config --add channels defaults % conda config --add...

My apologies for the delay, v. 3.1.1 should propagate the ETE3DBTAXAFILE variable correctly to all of the downstream functions and fix this issue