alvanuffelen

Sampling sequences by number is not truly random

3

### Prerequisites - [x] make sure you're are using the latest version by `seqkit version` - [x] read the [usage](http://bioinf.shenwei.me/seqkit/usage/) ### Describe your issue * [x] describe the problem When...

Error: Format error: Invalid varint encoding

2

Using the command with diamond v2.1.0: ` diamond blastx -q subsample.fq -d nr_cleaned.dmnd -o zymo.daa -F 15 -f 100 --range-culling --top 10 -p 64 -b12 ` I get the following...

Not all parameters of the taxonomy API work

3

https://api.ncbi.nlm.nih.gov/datasets/v2alpha/taxonomy/taxon/9606?returned_content=COMPLETE and https://api.ncbi.nlm.nih.gov/datasets/v2alpha/taxonomy/taxon/9606?returned_content=TAXIDS both return the same output. Should there be no difference between the two? The parameters under `filtered_subtree` also seem to have little effect.

Filter of ranks without order

5

### Prerequisites - [x] make sure you're are using the latest version by `taxonkit version` - [x] read the [usage](http://bioinf.shenwei.me/taxonkit/usage/) ### Describe your issue In the documentation, it mentions: >...

The longest text of the legend gets cut off when saved to SVG. ``` fig = go.Figure() fig.add_trace(go.Scatter( x=[1, 2, 3, 4, 5], y=[1, 2, 3, 4, 5], name="ShortTitle" ))...

Mean read quality calculation

5

The mean read quality is [calculated by](https://github.com/wdecoster/NanoPlot/blob/da7cd004a38093394f7847143145f23985e7daa6/nanomath/nanomath.py#L169): 1. Converting the mean phred quality score of each read to the base-calling error probability 2. Calculating the mean of all the mean...