Merge dev/documentation into develop

[emarinier]

This pull request updates the user and developer documentation for proksee (particularly proksee assemble).

The following files have been created or modified:

• README.md
• docs/assembled.md
• docs/developer/assemble/assemble.md
• docs/developer/assemble/data_structures.md
• docs/developer/overview

[jubileepower]

Please see my comments below, feel free to take or leave as you see fit. README.md:

• Regarding what Proksee is. Do we want to throw in keywords such as "assembly or quality metric assessment" (utilizing refseq database) and/or "expert system"? The nice and clean definition sounds more of the definition of Proksee cmd tools at the backend of Proksee, the expert system.
• "structural information" may lead to thinking of 3D structure.
• Relevant to the point above, "information" used seemed a bit vague to me. Would assessment or quality metrics work?

assembled.md:

• "appear to vary widely from what is expected for the assembled species": appear to deviate from what is expected for the assembled species. Deviation is currently defined as under 5th or above 95th percentiles of RefSeq-included assemblies for that species.
• "an overview of the assemblies produced during pipeline": assembly statistics?
• More of intro and a tool usage document than assemble.md under developer. Is there a better term for this markdown file?

assemble.md:

• "assembles the reads hastily": Just wondering if a different phrase would sound better.."provide a fast and draft assembly?"
• "no good assemble can be produced": no good assembly
• "using the SKESA assembler0": assembler
• At Create strategy, "The fast assembly metrics are compared against the sequence assembly database to see if the assembly metrics agree with what would be expect for the species". Do we need to note the time and source (refseq included) the assembly database was retrieved here, if the AssemblyDatabase CSV file will be posted.

data_structures.md:

• Very clear, thanks for clarifying the few spots Eric M.

overview.md

• Nice and clean.

PS. Arnab's ML component may need a markdown page in development down the road?

[emarinier]

Regarding what Proksee is. Do we want to throw in keywords such as "assembly or quality metric assessment" (utilizing refseq database) and/or "expert system"? The nice and clean definition sounds more of the definition of Proksee cmd tools at the backend of Proksee, the expert system.

At least with how things are organized right now, the README is for "proksee-cmd", the command-line component of component. This should include annotation and assemble, even though we've only done assemble.

I guess the somewhat confusing thing is that the README talks as though it's completely "assemble"-focused. I've tried to make the distinction a little bit more.

"structural information" may lead to thinking of 3D structure. Relevant to the point above, "information" used seemed a bit vague to me. Would assessment or quality metrics work?

Updated to be more clear.

assembled.md

Updated, except I'm not sure what you mean by:

More of intro and a tool usage document than assemble.md under developer. Is there a better term for this markdown file?

assemble.md

Updated.

Do we need to note the time and source (refseq included) the assembly database was retrieved here, if the AssemblyDatabase CSV file will be posted.

I'm going to postpone that for now, until we get a better sense of which databases will be used and where they're going to be stored.

PS. Arnab's ML component may need a markdown page in development down the road?

Yup! I agree.

[emarinier]

Note to add style instructions to developer documentation (i.e. Google Python style).

[ericenns]

👍 Looks good to me, I am going to merge this for now. The developer documentation regarding style can be added later.