erinyoung / roundabout

Finding regions of similarity between plasmids

Greetings!

I work at the Utah Public Health Laboratory as a Bioinformatician.

I mostly work in the linux (centos and ubuntu) command line (shell).

I have written a few packages in python, but mostly I cobble bioinformatic tools together into nextflow workflows.

I'd like to learn rust, but haven't found the time.

I'm almost always open for collaboration.

roundabout's Issues

Add ppanggolin

Pan genome graphs

gene of interest

Create a channel for a multifasta for genes of interest. These are used in a blast query and added to the amr radius either in the same bedfile or a second file (with a different color)

add test profile

There are fasta files IN THIS REPO for testing, it'd be simple to just include a profile that uses those files.

update readme

Like... I KNOW!!!

I need to include some more images.

add emboss?

might be easier to parse than dnadiff

DNA diff matrix

DNA diff is actually really useful to me. I think a matrix or some sort of file that includes coverage and identity would be helpful.

Add the whale's color scheme

https://www.sltrib.com/artsliving/2022/04/12/whale-rises-salt-lake/

because it's beautiful

Fails if no AMR gene found

There needs to be something in place to catch sequences that don't have AMR genes

Change pygenomeviz colors to greyscale

The slate blue color scheme isn't as useful as hoped.

I think the chromosomes can still be black, but then close matches as a darker grey and the inversions as a light grey would work better.

add pygenomeviz's pgv-simpleplot

This repo is really turning into a pygenomeviz stan account.

pygenomeviz has a new feature : simpleplot

I should probably include it.