Lee Katz

Invalid alleles and invalid genes

8

Hi, I am using ChewBBACA v3 and imported the EnteroBase Salmonella cgMLST scheme and got invalid genes. These are the steps I took. ```shell # get scheme: fasta + trn...

Hi @DerrickWood , I was having issues with my personal database where I edited my own taxonomy and where I needed to assess contigs instead of reads. Where I messed...

Need documentation on cgMLST

1

I am taking some notes on how I ran cgMLST, and I hope you can add documentation for it. Create database: this took a very long time ```bash # Downloaded...

Hi, I wanted to make EToKi more accessible. Relevant: #11 Therefore, I replaced usearch with blastp. Subsequently it has been containerized in the staph-b docker space. I have also attached...

--install --path

1

Hi, could you clarify in the documentation which things I can put into `--path`? Like if I have the entire spades package downloaded, do I just run it with `--path...

Added new yml workflow file that runs unit tests. Shows a nice checkmark in the repo if all tests passed. I only tested for the primary clade and clade. Click...

Hi, I wanted to see if you could update SRST2 to show compatibility against the latest versions of bowtie2. There have been several versions since the last update of SRST2,...

Add Sneakernet - a Quality Control pipeline for new reads

4

Describe your pull request here ---- Please read the [guidelines for Bioconda recipes](https://bioconda.github.io/contributor/guidelines.html) before opening a pull request (PR). ### General instructions * If this PR adds or updates a...

Parallelization

1

I was wondering if you are interested in parallelizing? Maybe there are some python packages that could help. I am simulating the genomes of a 1700-taxon tree and it's just...

Request: a script to figure out input parameters

1

This is kind of a long-term request since it is so difficult but probably very useful. I feel like it is possible to estimate many of the parameters in the...