Create tutorial scripts that show common use cases

[dkoslicki]

Motivation: I have colleagues who would like to use this tool, but for more than just generating taxonomic profiles. I would also like to utilize the resulting SAM files to do things like investigate horizontal gene transfer, look at structural variation, analyze bacterial evolution, etc.

Goal: create an assortment of bash scripts that show a variety of different ways in which this "reduce database and then align" paradigm can work.

Tasks: Create bash scripts that

• [ ] Show a simple local installation
• [ ] Show different ways to run the pipeline with different parameters and the results
• [ ] Show how to re-train everything using a custom database
• [ ] Show how to do the database subsetting and only return this subset database
• [ ] Show how to do the mapping, but don't return a taxonomic profile (eg. taxonomic information is unavailable or too difficult to create)

I welcome suggestions for other use cases as well.

This work will be performed in a different branch.

[luhugerth]

Hi! Simple question, related to the tutorial :) How does metalign treat paired reads? If two fastq files are given as input, will they be treated as paired? Does it matter what the name of the files is? Thanks!

[nlapier2]

Hi, thanks for your interest. Right now, we do not handle separate paired reads files; we instead require them to be interleaved first. Accepting separate paired files is a feature we'd like to add.