Nilad

Hi, First thank for this vital (now for me) tool. I only used it to the genus clade of Klebsiella. I propose to add (only justified by a tree analysis)...

Define Output Options for roary_plots.py

3

Hi, To render more conterable roary and the scripts associated, it is possible to add an option of "output directory" or "output path" to choose where saves the files produces...

Suggestion : Add length gene on Bokeh Spot frame

1

Hello =) It is possible to add just bellow the start and stop information field (and above to the gene name) on the Bokeh dynamic "gene" frame the length of...

Hi, I had encounter a case with a SNP not detected by Snippy on a strain (call it 'toto'). After running Snippy-core (with "toto"), the resulting ".vcf" show for this...

Hi, Recently, i notice that few Profile like ST-2724 in "Acinetobacter baumannii#1" schema or ST-2609 in "Haemophilus influenzae" schema contains "N" letter index instead of allele index. So i got...

Input file - similarity matrix

1

Hi, Second issue to enhance this tools =) Most People use differents tools for ANI score like OrthoANI or want to use AAI score or mash distance values, all theses...

Actually, the function https://github.com/sanger-pathogens/ariba/blob/master/ariba/pubmlst_getter.py#L24 with "http://pubmlst.org/data/dbases.xml" dont take the actual pubMLST database listing -> https://rest.pubmlst.org/ Have a good day.

Domain cut in SVG

3

Hi, First thank for this pretty scalable tool in D3. At the load of the graph the domains are cut like that...  ... Of course in the page it's...

RuntimeWarning: pysam.libcalignedsegment.PileupColumn size changed, may indicate binary incompatibility. Expected 72 from C header, got 88 from PyObject

3

Same issue than #105 I install `pysamstats` on Singularity container. I tried multiples version of `pysamstats`, `cython`, `pysam` with `pip` and with `conda` without succes. Here my last try, if...