diff --git a/.release-please-manifest.json b/.release-please-manifest.json
index 2be9c43c8..0ee8c0128 100644
--- a/.release-please-manifest.json
+++ b/.release-please-manifest.json
@@ -1,3 +1,3 @@
 {
-  ".": "0.2.0"
+  ".": "0.3.0"
 }
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 99852f4e6..4c8599b7d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,18 @@
 
 All notable changes to this project will be documented in this file.
 
+## [0.3.0](https://github.com/fiberseq/FIRE/compare/v0.2.0...v0.3.0) (2026-08-15)
+
+
+### Features
+
+* per-sample reference support via manifest ref/ref_name columns ([#71](https://github.com/fiberseq/FIRE/issues/71)) ([6e1c24e](https://github.com/fiberseq/FIRE/commit/6e1c24e2b6fe0d81b2df6abdb1ca8b03b690fbbe))
+
+
+### Refactoring
+
+* remove the unused leviosam2 chain-lift rules ([#70](https://github.com/fiberseq/FIRE/issues/70)) ([150d68e](https://github.com/fiberseq/FIRE/commit/150d68e963f50c441f319a90e8239d52bf45ee70))
+
 ## [0.2.0](https://github.com/fiberseq/FIRE/compare/v0.1.3...v0.2.0) (2026-08-14)
 
 
diff --git a/pixi.toml b/pixi.toml
index 9e1d148a5..93e042c4a 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -4,7 +4,7 @@ channels = ["conda-forge", "bioconda"]
 description = "A Snakemake pipeline for calling FIRE peaks using fibertools-rs."
 name = "FIRE"
 platforms = ["osx-arm64", "linux-64"]
-version = "0.2.0"
+version = "0.3.0"
 
 [tasks]
 fmt = "ruff format . && taplo format pixi.toml && snakefmt workflow/"