update readme

README.md

@@ -2,15 +2,19 @@
 
 Discover and annotate the virome
 
-`Cenote-Taker 3` is a bioinformatics tool that scales from individual genomes sequences to massive metagenome assemblies to:
+![Logo](images/cenote-taker_3_logo.png)
+
+Works on your laptop or HPC (compatible with MacOS and Linux)
+
+`Cenote-Taker 3` is a virus bioinformatics tool that scales from individual genomes sequences to massive metagenome assemblies to:
 
 1)  Identify sequences containing genes specific to viruses (virus hallmark genes)
 
 2)  Annotate virus sequences including:
 
 ---a) adaptive ORF calling
 
----b) a large catalog of HMMs from virus gene families
+---b) a large catalog of HMMs from virus gene families for functional annotation
 
 ---c) Hierarchical taxonomy assignment based on hallmark genes
 
@@ -20,6 +24,14 @@ Discover and annotate the virome
 
 **Also, `Cenote-Taker 3` is very fast, many many times faster than `Cenote-Taker 2`, and faster than comparable annotation using `pharokka` (in my hands)**
 
+Image of example genome map:
+
+![Map](images/genome_map1.png)
+
+## Schematic
+
+![Schematic](images/cenote-taker_3_schematic.png)
+
 ## Installation Instructions
 
 *A bioconda package is forthcoming, but this is considered a beta build, so I'm holding off on that*
@@ -30,34 +42,55 @@ Discover and annotate the virome
 
 2)  Using `mamba` (package manager within `conda`) and the provided yaml file, make the environment:
 
-`mamba env create -f Cenote-Taker3/environment/ct3_beta_env.yaml`
+`mamba env create -f Cenote-Taker3/environment/ct3_env.yaml`
 
 *Versions used in test installations*
 
 mamba 1.5.1
 
 conda 23.7.4
 
-
 3)  Activate the conda environment.
 
-`conda activate ct3_beta`
+`conda activate ct3_env`
 
 4)  Change to repo and `pip` install command line tool.
 
 `cd Cenote-Taker3`
 
 `pip install .`
 
-*You should be able to type `cenotetaker3` in terminal to bring up help menu now*
+*You should be able to type `cenotetaker3` and 'get_ct3_dbs' in terminal to bring up help menu now*
 
 5)  Change to a directory where you'd like to install databases and run database script, specify DB directory with `-o`.
 
 *Total DB file size of 3.0 GB after file decompression*
 
 `cd ..`
 
-`python Cenote-Taker3/src/cenote/get_ct3_databases.py -o ct3_DBs --hmm T --mmseqs_tax T --mmseqs_cdd T --domain_list T`
+`get_ct3_dbs -o ct3_DBs --hmm T --mmseqs_tax T --mmseqs_cdd T --domain_list T`
+
+<details>
+
+  <summary>With optional hhsuite databases</summary>
+
+  Warning: due to inconsistent server speed, these downloads may take over 2 hours.
+
+  You may download one or more hhsuite DB.
+
+  The data footprint is:
+
+  | Database | Size   |
+  |----------|--------|
+  | CDD      | 6.1 GB |
+  | pfam     | 4.6 GB |
+  | pdb70    | 56 GB  |
+
+  ```         
+  get_ct3_dbs -o ct3_DBs --hmm T --mmseqs_tax T --mmseqs_cdd T --domain_list T --hhCDD T --hhPFAM T --hhPDB T
+  ```
+
+</details>
 
 6)  Set the database directory as a conda environmental variable.
 
@@ -69,50 +102,74 @@ conda 23.7.4
 
 ### Help Menu
 
-```
+```         
 cenotetaker3 -h
 ```
 
-
 ### Test contigs
 
-```
+```         
 cenotetaker3 -c Cenote-Taker3/test_data/testcontigs_DNA_ct2.fasta -r test_ct3 -p T
 ```
 
 ### Default Discover and Annotate
 
-```
+```         
 cenotetaker3 -c my_metagenome_contigs.fna -r my_meta_ct3 -p T
 ```
 
-### Discover and Annotate, Force `prodigal` (faster)
+### Discover and Annotate, Force `prodigal` (prodigal-gv is default)
 
-```
+```         
 cenotetaker3 -c my_metagenome_contigs.fna -r my_meta_ct3pr -p T --caller prodigal
 ```
 
 ### Just Annotate
 
-```
+```         
 cenotetaker3 -c my_virus_contigs.fna -r my_virs_ct3 -p F -am T
 ```
 
-### Notes
-
-`Cenote-Taker 3` is under active development, so please open an issue if anything seems unusual or any errors occur. It's likely that I've not tested every parameter combination, and bugs will be a simple fix.
+### Choose which HMM DBs are hallmark (virion rdrp is default)
 
+```         
+cenotetaker3 -c my_metagenome_contigs.fna -r my_meta_ct3 -p T -db virion rdrp dnarep
+```
 
-### To-do list
+### Calculate coverage level with reads
 
-* Add module to use `HHsearch` for gene annotation
+```         
+cenotetaker3 -c my_metagenome_contigs.fna -r my_meta_ct3 -p T --reads my_reads/*fastq
+```
 
-* Add RDRP database as option for virus discovery
+## Output Files
+
+``` {style="color: blue"}
+{run_title}/
+|   {run_title}_virus_summary.tsv   <- main summary file for each virus
+|   {run_title}_virus_sequences.fna   <- all virus genome seqs
+|   {run_title}_virus_AA.faa   <- all virus AA seqs
+|   {run_title}_prune_summary.tsv   <- summary of pruning of each sequence
+|   final_genes_to_contigs_annotation_summary.tsv   <- annotation info, all genes
+|   run_arguments.txt   <- arguments used in this run
+│   {run_title}_cenotetaker.log   <- main log file
+│
+└───sequin_and_genome_maps/
+│   │   {run_title}*gbf   <- genome maps
+│   │   {run_title}*fsa   <- genome sequence
+│   │   {run_title}*gtf   <- feature table gtf format
+│   │   {run_title}*tbl   <- feature table sequin format
+│   │   {run_title}*sqn   <- non-human-readable sequin file for GenBank sub
+│   │   {run_title}*cmt   <- sequin comment file
+│
+└───ct_processing/
+│   │   --- many intermediate files ---
+```
 
-* Nucleotide or kmer-based species-level taxonomy
+### Notes
 
-* Incorporate `prodigal-gv` as alternative ORF caller
+`Cenote-Taker 3` is under active development, so please open an issue if anything seems unusual or any errors occur. It's likely that I've not tested every parameter combination, and bugs will be a simple fix.
 
-* Update HMM database to increase consistency of names/functions between similar models
+### To-do list
 
-* instructions for manual curation -> GenBank deposit of `Cenote-Taker 3` output
+-   instructions for manual curation -\> GenBank deposit of `Cenote-Taker 3` output