add more details to docs

docs/README.md

@@ -1,7 +1,13 @@
 Bin Chicken
 =============
 
-Bin Chicken is a tool that performs targeted recovery of low abundance metagenome assembled genomes through intelligent coassembly.
+Bin Chicken is a tool that performs targeted recovery of low abundance metagenome assembled genomes through strategic coassembly.
+
+It maximises recovery of novel diversity by automatically identifying sets of samples for coassembly and co-binning.
+In particular, it identifies groups of samples sharing novel marker genes that are predicted to have sufficient combined coverage for assembly and recovery of their associated genomes (10X minimum).
+Identical matching of sequence windows is used to reduce the risk of forming chimeric bins from near-relatives.
+
+It is currently designed to use metagenomic data sequenced using Illumina short-read technology.
 
 ![Bin Chicken workflow](/workflow.png)
 
@@ -29,3 +35,18 @@ binchicken iterate \
   --run-aviary --assemble-unmapped \
   --cores 64 --output binchicken_3_coassembly
 ```
+
+## Help
+
+If you have any questions or need help, please [open an issue](https://github.com/AroneyS/binchicken/issues).
+
+## License
+
+Bin Chicken is licensed under [GPL3 or later](https://gnu.org/licenses/gpl.html).
+The source code is available at [https://github.com/AroneyS/binchicken](https://github.com/AroneyS/binchicken).
+
+## Citation
+
+Samuel T. N. Aroney, Rhys J. P. Newell, Gene W. Tyson and Ben J. Woodcroft.
+Bin Chicken: targeted metagenomic coassembly for the efficient recovery of novel genomes.
+bioRxiv (2024): 2024-11. https://doi.org/10.1101/2024.11.24.625082

docs/installation.md

@@ -7,6 +7,13 @@ Installation
 
 There are several ways to install Bin Chicken
 
+## System requirements
+
+The purpose of Bin Chicken is to suggest sets of samples for coassembly.
+The coassembly process can use upwards of 250GB of RAM and 32 cores, so we recommend running on a HPC system if you intend to assemble and recover genomes.
+
+Bin Chicken is supported for Linux (tested on SUSE 12.5). Specific dependencies are listed in [binchicken.yml](https://github.com/AroneyS/binchicken/blob/master/binchicken.yml).
+
 ## Install from Bioconda
 
 Install latest release via bioconda.
@@ -34,3 +41,21 @@ conda env create -f binchicken.yml
 conda activate binchicken
 pip install -e .
 ```
+
+### Testing and demo
+
+Tests can be run if installed from source to ensure Bin Chicken is installed correctly.
+The subcommand tests can take upwards of 30 minutes to complete using a single thread.
+The manual tests can take multiple days to complete, using 64 threads.
+
+```bash
+# Test single subcommand
+python test/test_single.py
+# Test coassemble subcommand
+python test/test_coassemble.py
+# Test iterate subcommand
+python test/test_iterate.py
+
+# Test downloading and coassembly/recovery with Aviary. Results stored in example/test_* directories.
+python test/test_manual.py
+```

docs/setup.md

@@ -7,6 +7,7 @@ Environment setup
 
 Bin Chicken uses separate conda environments for each subprocess.
 Run `binchicken build` to create those subprocess conda environments and setup environment variables.
+This can take upwards of 30 minutes to complete, depending on the speed of your internet connection.
 
 Conda prefix is the directory you want to contain the subprocess conda environments.
 SingleM metapackage is the metapackage downloaded by SingleM using `singlem data` (see <https://github.com/wwood/singlem>).