DOC: Update docs

Vini2 · Nov 26, 2022 · e7f2b73 · e7f2b73
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diff --git a/docs/install.md b/docs/install.md
@@ -1,5 +1,7 @@
 # Setting up Phables
 
+Phables is now available on PyPI at [https://pypi.org/project/phables/](https://pypi.org/project/phables/). If you directly installed Phables from [PyPI](https://pypi.org/project/phables/), you can skip the next two steps and go to [Setting up Gurobi](#setting-up-gurobi).
+
 ## Downloading Phables
 
 You can clone the Phables repository to your machine.

diff --git a/docs/preprocess.md b/docs/preprocess.md
@@ -26,6 +26,9 @@ The `assembly_graph.gfa` file contains the unitig sequences which should be extr
 
 ```bash
 python gfa2fasta.py --graph assembly_graph.gfa --assembler flye --output <output_folder>
+
+# If you installed using pip
+gfa2fasta --graph assembly_graph.gfa --assembler flye --output <output_folder>
 ```
 
 ## Step 3: Map reads to unitig sequences and get BAM files
@@ -59,6 +62,9 @@ This command will produce a coverage file for each sample. You can combine the c
 
 ```bash
 python combine_cov.py --covpath coverage_rpkm --output <output_path>
+
+# If you installed using pip
+combine_cov --covpath coverage_rpkm --output <output_path>
 ```
 
 The output file will be `coverage.tsv` where each row represents a unitig and each column represents a sample.