Genosysmics.md

 # Genosysmics #
 
-Genosysmics recovers genes and mags from metagenomics assemblies and construct annotated collections. 
+Genosysmics recovers genes and mags from metagenomic assemblies and construct annotated collections. 
 
 ## Quickstart ##
 
+### Install and initialization ###
 ``` 
 git clone <genosysmics repo>
 conda create -n genosys python=3.7
 conda activate genosis
 cd genosysmics
 pip install.
-
-
 cd ../<working_dir>
 genosysmics init <sample_dir>
-genosysmics run all **snakemake.args # for a local execution
-genosysmics run all --profile config/sge/ # for execution on age
+```
+
+### Genes collection ###
 
 ```
+genosysmics run genes **snakemake.args (--profile config/sge/) # for a local execution
+``` 
+
+**Expected output**
 
+```
+genes_collection
+             ├── all_prot.aa.c95.faa
+             ├── all_prot.nucleotide.c95.fnn
+             ├── all_prot.nucleotide.fnn
+             ├── mapping
+             │   ├── bams/
+             └── tables
+                 ├── bp_covered.tsv
+                 ├── genes_abundance.tsv
+                 ├── genes_functions.tsv
+                 ├── genes_length.tsv
+                 ├── genes_taxo.UniRef50.tsv
+                 └── reads_counts.tsv
+```
+
+### Genomes collection ###
+```
+genosysmics run genomes **snakemake.args (--profile config/sge/) # for execution on age
+```
+
+**Expected output**
+
+genomes_collection/
+├── all_genomes.0.95.fa.gz
+├── all_genomes.0.99.fa.gz
+├── annotation
+│   ├── functions
+│   │   └── <genomes>/
+│   └── taxonomy/
+│       ├── align/
+│       ├── classify/
+│       └── identify/
+├── data
+│   ├── checkM/
+│   └── drep/
+├── dereplicated_at_0.95
+│   └── <genomes>.fa
+├── dereplicated_at_0.99
+│   └── <genomes>.fa
+├── mapping
+│   ├── bam/
+└── tables
+    ├── bp_covered.0.95.tsv
+    ├── bp_covered.0.99.tsv
+    ├── genomes_abundance.0.95.tsv
+    ├── genomes_abundance.0.99.tsv
+    ├── genomes_functions.tsv
+    ├── genomes_length.tsv
+    ├── gtdbtk.ar122.bac120.summary.tsv
+    ├── reads_counts.0.95.tsv
+    └── reads_counts.0.99.tsv
+
+```
 
 ## Current workflow ##
 ![dag_all.svg](uploads/7c013867df4b500100be22a8d1fabcbb/dag_all.svg)