Improve manual

[mikolmogorov]

Make sure that the current manual is up to date. See https://github.com/KolmogorovLab/hapdup for a template what to include. Docker package is optional, I would instead prefer an easy-to-follow conda installation.

In addition, let's have a small test case uploaded somewhere (e.g. zenodo.org), so that anyone can easily reproduce the commands and try metaPhase on their machine. Example here: https://github.com/fenderglass/Flye/blob/flye/docs/USAGE.md#-examples

[mikolmogorov]

Also minimum software version should be specified, e.e. samtools>=1.14, bcftools>=1.14.

[mikolmogorov]

From todays discussion, there are two priorities here:

• Make a small test example upload it to zenodo.org, and describe a set of commands to download and run it.
• Describe the installation via conda. Describe how to create a new environment from scratch that will be sufficient to run. You can do it either though a command line example (that a user would copy) or a conda environemnt file. Overall, this should also be a set of terminal commands that user can copy and execute (given that conda is installed)

[mikolmogorov]

• another important moment: provide commands to transition from the initial gfa to fasta generating bam alignment.

[katerinakazantseva]

done