Lee Katz

Visualize Midas results

3

Hi, I am asking this as a third party. I was wondering if you could help with Midas visualization. I want to suggest to _others_ that they should visualize their...

**Describe the bug** Hi, `preparing the database` is in the outline, but I don't see it in the README. Can you add it?  Thank you!

Profile file for cgMLST

3

Hi, related to #11, could you show me what a profile file should look like for cg/wgMLST? I downloaded the wgMLST scheme from the ChewBBACA website and I want to...

Interleaved fastq file

1

I think related to #3 (?), how would you parse an interleaved fastq file? Where read 1 is the first entry of the file and read 2 is the second...

Error reading tree number 1: Closing bracket missing.

3

Similar to #9 but I can't solve it with regex. I downloaded the nextstrain tree (Jan 4, 2021) for nCov and wanted to run TreeToReads.py with it (newick attached below)....

There are a lot of dependencies in the README and so I put a dependency check into the main script

Update Kalamari

7

* Added more informative messages into .messages.txt to explain how to build Kalamari databases * It was using `curl` to pull individual files from the source repo. Now it copies...

Add colorid

1

Add ColorID `Experiments with using BIGSI data structure for metagenomic and QC applications` ---- Please read the [guidelines for Bioconda recipes](https://bioconda.github.io/contributor/guidelines.html) before opening a pull request (PR). ### General instructions...

mapping input contig names to output

6

Given that I get a contig name like `RNODE_1_length_2185_cov_1230.39000`, how would I know which contig that is in the original file? I can search the coverage field `1230.39` to find...

best assembler for the job?

1

Hi, I was wondering what assembler the authors recommend before running Recycler. It seems like spades is recommended, but then I was also wondering what parameters you would recommend. Is...