Three very minor typos are present in these documents that break the code when copied-and-pasted as they are.

Link: https://gatk.broadinstitute.org/hc/en-us/community/posts/360056484652-Typos-in-docs

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1.  https://gatk.broadinstitute.org/hc/en-us/articles/360036726571-LeftAlignAndTrimVariants

the fifth code block on this page

Spades produces many short contigs. It may be helpful to have an optional parameter for metagenomics.py::assemble_spades, perhaps --minContigLength, to only write contigs greater in length than a specified value.

The README.md is better formated and gives a nive front page on github. As part of this, the contents may also be revised.

For example, I just compiled augustus from scratch in a clean Ubuntu VM. Finding all the dependencies to install with apt-get in the readme was a bit annoying.

I suggest to extend the readme with an apt-get statement that installs dependencies. This is also a precursor

Write a concise user manual using sphinx and make is available at readthedocs.
The audience should be primarily bioinformaticians.
The scope should coverL

• installing variant spark
• running importance analysis with command line an python APIs
• references for available functions and options
• running on cluster and clouds (AWS, Databricks)
• a simple developer guide (building testing).