readme

README.md

@@ -1,15 +1,51 @@
 # Quadram Institute MetaBarcoding Analysis
 
-![Qimba Logo](./assets/qimba.svg)
+![Qimba Logo](./assets/qimba-header.svg)
 
 A toolkit to support Metabarcoding Analysis
 
+Qimba comes with a set of subcommands, that you can list running `qimba`:
+
+```text
+Usage: qimba [OPTIONS] COMMAND [ARGS]...
+
+  Qimba - Bioinformatics Toolkit
+
+  A modular toolkit for bioinformatics analysis with focus on amplicon
+  processing.
+
+Options:
+  --config PATH  Path to config file
+  --help         Show this message and exit.
+
+Sample Management:
+  make-mapping  Generate a sample mapping file from a...
+  show-samples  Display sample information from a mapping...
+
+Sequence Processing:
+  derep  Dereplicate FASTA sequences using USEARCH.
+
+Format conversions and manipulation:
+  dada2-split  Split DADA2 TSV file into FASTA and...
+
+File Operations:
+  check-tab  Check TSV files for their dimensions and...
+
+Utility Commands:
+  version  Print the version of Qimba.
+```
+
+## Configuration file
+
+Some defaults can be set in your `~/.config/qimba.ini` file:
+
+
 Example configuration:
 ```ini
 [qimba]
 default_output_dir = .
 threads = 4
 
-[assign-tax]
+[subcommand name]
 database = /path/to/database
 ```