update readme

Author: ayobi

.gitignore

@@ -49,3 +49,4 @@ ITSx_temp_directory__*
 !testdata/*.fa
 !testdata/*.fna
 
+data/figures/

README.md

@@ -54,6 +54,14 @@ This produces `results/sample1.its1.fasta`, `results/sample1.its2.fasta`, and `r
 
 ## Install
 
+### Bioconda (recommended)
+
+ITSxRust is available on [Bioconda](https://bioconda.github.io/). This is the easiest way to install, as it also handles the HMMER dependency:
+
+```bash
+conda install -c bioconda -c conda-forge itsxrust
+```
+
 ### Prebuilt binaries
 
 Download the binary for your platform from [GitHub Releases](https://github.com/ayobi/ITSxRust/releases), then:
@@ -90,7 +98,7 @@ ITSxRust calls `nhmmer` to search profile-HMMs against input sequences. Install
 conda install -c bioconda hmmer
 ```
 
-The Docker image includes HMMER, so no separate installation is needed when using the container.
+> **Note:** If you installed via Bioconda or Docker, HMMER is already included — no separate installation is needed.
 
 ### HMM profiles
 
@@ -204,7 +212,7 @@ bench/         Benchmarking + simulation harness
 
 ## Roadmap
 
-- Bioconda recipe
+- ~~Bioconda recipe~~ ✅
 - In-process HMM bindings (replace nhmmer subprocess)
 
 ## License

data/figures/fig3_boundary_errors.pdf

@@ -65,7 +65,7 @@ def main():
     fig, axes = plt.subplots(2, 3, figsize=(12, 6.5),
                               gridspec_kw={'height_ratios': [1, 1]})
     fig.subplots_adjust(hspace=0.35, wspace=0.28, left=0.07, right=0.97,
-                        top=0.92, bottom=0.08)
+                        top=0.88, bottom=0.08)
 
     # ── Row 1: Box plots (capped at 100bp for visibility) ──
     CAP = 100
@@ -137,8 +137,8 @@ def main():
         if j == 0:
             ax.legend(fontsize=7, loc='lower right', framealpha=0.9)
 
-    fig.suptitle('Boundary accuracy on simulated ONT reads', fontsize=12,
-                 fontweight='bold', y=0.97)
+    fig.suptitle('Boundary accuracy on simulated ONT reads', fontsize=14,
+                 fontweight='bold', y=0.98)
 
     plt.savefig(f'{args.outfile}.pdf', dpi=300, bbox_inches='tight')
     plt.savefig(f'{args.outfile}.png', dpi=300, bbox_inches='tight')