diff --git a/Cargo.lock b/Cargo.lock
index b0726dd..bf0ca5f 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -23,15 +23,6 @@ version = "1.0.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe"
 
-[[package]]
-name = "aho-corasick"
-version = "1.0.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "67fc08ce920c31afb70f013dcce1bfc3a3195de6a228474e45e1f145b36f8d04"
-dependencies = [
- "memchr",
-]
-
 [[package]]
 name = "android-tzdata"
 version = "0.1.1"
@@ -96,21 +87,6 @@ dependencies = [
  "windows-sys 0.48.0",
 ]
 
-[[package]]
-name = "anyhow"
-version = "1.0.71"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9c7d0618f0e0b7e8ff11427422b64564d5fb0be1940354bfe2e0529b18a9d9b8"
-
-[[package]]
-name = "approx"
-version = "0.5.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "cab112f0a86d568ea0e627cc1d6be74a1e9cd55214684db5561995f6dad897c6"
-dependencies = [
- "num-traits",
-]
-
 [[package]]
 name = "arrayvec"
 version = "0.5.2"
@@ -144,73 +120,6 @@ version = "0.21.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "a4a4ddaa51a5bc52a6948f74c06d20aaaddb71924eab79b8c97a8c556e942d6a"
 
-[[package]]
-name = "bio"
-version = "1.1.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e07645dcc036557a09cf078268b4666f0ce737bd797b0ee554de29ea81981ab2"
-dependencies = [
- "anyhow",
- "approx",
- "bio-types",
- "bit-set",
- "bv",
- "bytecount",
- "csv",
- "custom_derive",
- "enum-map",
- "fxhash",
- "getset",
- "itertools 0.10.5",
- "itertools-num",
- "lazy_static",
- "multimap",
- "ndarray",
- "newtype_derive",
- "num-integer",
- "num-traits",
- "ordered-float",
- "petgraph",
- "rand",
- "regex",
- "serde",
- "serde_derive",
- "statrs",
- "strum 0.24.1",
- "strum_macros 0.24.3",
- "thiserror",
- "triple_accel",
- "vec_map",
-]
-
-[[package]]
-name = "bio-types"
-version = "0.13.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "dfa990f40a28735fa598dc3dd58d73e62e6b41458959d623903b927ba7b04c80"
-dependencies = [
- "derive-new",
- "lazy_static",
- "regex",
- "strum_macros 0.24.3",
- "thiserror",
-]
-
-[[package]]
-name = "bit-set"
-version = "0.5.3"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "0700ddab506f33b20a03b13996eccd309a48e5ff77d0d95926aa0210fb4e95f1"
-dependencies = [
- "bit-vec",
-]
-
-[[package]]
-name = "bit-vec"
-version = "0.6.3"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "349f9b6a179ed607305526ca489b34ad0a41aed5f7980fa90eb03160b69598fb"
-
 [[package]]
 name = "bitflags"
 version = "1.3.2"
@@ -229,22 +138,6 @@ version = "3.12.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "3c6ed94e98ecff0c12dd1b04c15ec0d7d9458ca8fe806cea6f12954efe74c63b"
 
-[[package]]
-name = "bv"
-version = "0.11.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8834bb1d8ee5dc048ee3124f2c7c1afcc6bc9aed03f11e9dfd8c69470a5db340"
-dependencies = [
- "feature-probe",
- "serde",
-]
-
-[[package]]
-name = "bytecount"
-version = "0.6.3"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "2c676a478f63e9fa2dd5368a42f28bba0d6c560b775f38583c8bbaa7fcd67c9c"
-
 [[package]]
 name = "bytemuck"
 version = "1.13.1"
@@ -324,7 +217,7 @@ dependencies = [
  "heck",
  "proc-macro2",
  "quote",
- "syn 2.0.32",
+ "syn",
 ]
 
 [[package]]
@@ -438,44 +331,6 @@ dependencies = [
  "cfg-if",
 ]
 
-[[package]]
-name = "csv"
-version = "1.2.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "0b015497079b9a9d69c02ad25de6c0a6edef051ea6360a327d0bd05802ef64ad"
-dependencies = [
- "csv-core",
- "itoa",
- "ryu",
- "serde",
-]
-
-[[package]]
-name = "csv-core"
-version = "0.1.10"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "2b2466559f260f48ad25fe6317b3c8dac77b5bdb5763ac7d9d6103530663bc90"
-dependencies = [
- "memchr",
-]
-
-[[package]]
-name = "custom_derive"
-version = "0.1.7"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ef8ae57c4978a2acd8b869ce6b9ca1dfe817bff704c220209fdef2c0b75a01b9"
-
-[[package]]
-name = "derive-new"
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-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "3418329ca0ad70234b9735dc4ceed10af4df60eff9c8e7b06cb5e520d92c3535"
-dependencies = [
- "proc-macro2",
- "quote",
- "syn 1.0.109",
-]
-
 [[package]]
 name = "either"
 version = "1.9.0"
@@ -497,26 +352,6 @@ dependencies = [
  "cfg-if",
 ]
 
-[[package]]
-name = "enum-map"
-version = "1.1.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e893a7ba6116821058dec84a6fb14fb2a97cd8ce5fd0f85d5a4e760ecd7329d9"
-dependencies = [
- "enum-map-derive",
-]
-
-[[package]]
-name = "enum-map-derive"
-version = "0.6.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "84278eae0af6e34ff6c1db44c11634a694aafac559ff3080e4db4e4ac35907aa"
-dependencies = [
- "proc-macro2",
- "quote",
- "syn 1.0.109",
-]
-
 [[package]]
 name = "env_logger"
 version = "0.10.0"
@@ -581,12 +416,6 @@ dependencies = [
  "simd-adler32",
 ]
 
-[[package]]
-name = "feature-probe"
-version = "0.1.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "835a3dc7d1ec9e75e2b5fb4ba75396837112d2060b03f7d43bc1897c7f7211da"
-
 [[package]]
 name = "fixedbitset"
 version = "0.4.2"
@@ -672,38 +501,17 @@ dependencies = [
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 ]
 
-[[package]]
-name = "fxhash"
-version = "0.2.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c31b6d751ae2c7f11320402d34e41349dd1016f8d5d45e48c4312bc8625af50c"
-dependencies = [
- "byteorder",
-]
-
 [[package]]
 name = "getrandom"
-version = "0.2.9"
+version = "0.2.11"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c85e1d9ab2eadba7e5040d4e09cbd6d072b76a557ad64e797c2cb9d4da21d7e4"
+checksum = "fe9006bed769170c11f845cf00c7c1e9092aeb3f268e007c3e760ac68008070f"
 dependencies = [
  "cfg-if",
  "libc",
  "wasi",
 ]
 
-[[package]]
-name = "getset"
-version = "0.1.2"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e45727250e75cc04ff2846a66397da8ef2b3db8e40e0cef4df67950a07621eb9"
-dependencies = [
- "proc-macro-error",
- "proc-macro2",
- "quote",
- "syn 1.0.109",
-]
-
 [[package]]
 name = "gimli"
 version = "0.27.2"
@@ -934,15 +742,6 @@ dependencies = [
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 ]
 
-[[package]]
-name = "itertools"
-version = "0.10.5"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b0fd2260e829bddf4cb6ea802289de2f86d6a7a690192fbe91b3f46e0f2c8473"
-dependencies = [
- "either",
-]
-
 [[package]]
 name = "itertools"
 version = "0.12.0"
@@ -952,15 +751,6 @@ dependencies = [
  "either",
 ]
 
-[[package]]
-name = "itertools-num"
-version = "0.1.3"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a872a22f9e6f7521ca557660adb96dd830e54f0f490fa115bb55dd69d38b27e7"
-dependencies = [
- "num-traits",
-]
-
 [[package]]
 name = "itoa"
 version = "1.0.6"
@@ -997,12 +787,6 @@ version = "0.2.150"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "89d92a4743f9a61002fae18374ed11e7973f530cb3a3255fb354818118b2203c"
 
-[[package]]
-name = "libm"
-version = "0.2.7"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f7012b1bbb0719e1097c47611d3898568c546d597c2e74d66f6087edd5233ff4"
-
 [[package]]
 name = "linux-raw-sys"
 version = "0.4.11"
@@ -1029,16 +813,6 @@ dependencies = [
  "num-traits",
 ]
 
-[[package]]
-name = "matrixmultiply"
-version = "0.3.7"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "090126dc04f95dc0d1c1c91f61bdd474b3930ca064c1edc8a849da2c6cbe1e77"
-dependencies = [
- "autocfg",
- "rawpointer",
-]
-
 [[package]]
 name = "memchr"
 version = "2.6.3"
@@ -1091,44 +865,6 @@ dependencies = [
  "windows-sys 0.45.0",
 ]
 
-[[package]]
-name = "multimap"
-version = "0.8.3"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e5ce46fe64a9d73be07dcbe690a38ce1b293be448fd8ce1e6c1b8062c9f72c6a"
-dependencies = [
- "serde",
-]
-
-[[package]]
-name = "nalgebra"
-version = "0.29.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d506eb7e08d6329505faa8a3a00a5dcc6de9f76e0c77e4b75763ae3c770831ff"
-dependencies = [
- "approx",
- "matrixmultiply",
- "nalgebra-macros",
- "num-complex",
- "num-rational",
- "num-traits",
- "rand",
- "rand_distr",
- "simba",
- "typenum",
-]
-
-[[package]]
-name = "nalgebra-macros"
-version = "0.1.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "01fcc0b8149b4632adc89ac3b7b31a12fb6099a0317a4eb2ebff574ef7de7218"
-dependencies = [
- "proc-macro2",
- "quote",
- "syn 1.0.109",
-]
-
 [[package]]
 name = "native-tls"
 version = "0.2.11"
@@ -1148,34 +884,43 @@ dependencies = [
 ]
 
 [[package]]
-name = "ndarray"
-version = "0.15.6"
+name = "noodles"
+version = "0.59.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "adb12d4e967ec485a5f71c6311fe28158e9d6f4bc4a447b474184d0f91a8fa32"
+checksum = "254ff100d92851724c8b271d6dccd3f21bb7be8438413995d67dcca3f996f2ac"
 dependencies = [
- "matrixmultiply",
- "num-complex",
- "num-integer",
- "num-traits",
- "rawpointer",
+ "noodles-core",
+ "noodles-fasta",
 ]
 
 [[package]]
-name = "newtype_derive"
-version = "0.1.6"
+name = "noodles-bgzf"
+version = "0.25.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ac8cd24d9f185bb7223958d8c1ff7a961b74b1953fd05dba7cc568a63b3861ec"
+checksum = "7d578e5a173cbfac77295db4188c959966ce24a3364e009d363170d1ed44066a"
 dependencies = [
- "rustc_version",
+ "byteorder",
+ "bytes",
+ "crossbeam-channel",
+ "flate2",
 ]
 
 [[package]]
-name = "num-complex"
-version = "0.4.3"
+name = "noodles-core"
+version = "0.12.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "94fbe3192fe33acacabaedd387657f39b0fc606f1996d546db0dfe14703b843a"
+
+[[package]]
+name = "noodles-fasta"
+version = "0.30.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "02e0d21255c828d6f128a1e41534206671e8c3ea0c62f32291e808dc82cff17d"
+checksum = "310dcfb61e8e2cafb65d9da4b329a98a390f2b570c17599a7f4639328cfb3e2c"
 dependencies = [
- "num-traits",
+ "bytes",
+ "memchr",
+ "noodles-bgzf",
+ "noodles-core",
 ]
 
 [[package]]
@@ -1206,7 +951,6 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "578ede34cf02f8924ab9447f50c28075b4d3e5b269972345e7e0372b38c6cdcd"
 dependencies = [
  "autocfg",
- "libm",
 ]
 
 [[package]]
@@ -1263,7 +1007,7 @@ checksum = "a948666b637a0f465e8564c73e89d4dde00d72d4d473cc972f390fc3dcee7d9c"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.32",
+ "syn",
 ]
 
 [[package]]
@@ -1294,15 +1038,6 @@ dependencies = [
  "vcpkg",
 ]
 
-[[package]]
-name = "ordered-float"
-version = "3.7.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "2fc2dbde8f8a79f2102cc474ceb0ad68e3b80b85289ea62389b60e66777e4213"
-dependencies = [
- "num-traits",
-]
-
 [[package]]
 name = "owned_ttf_parser"
 version = "0.15.2"
@@ -1318,12 +1053,6 @@ version = "3.5.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "c1b04fb49957986fdce4d6ee7a65027d55d4b6d2265e5848bbb507b58ccfdb6f"
 
-[[package]]
-name = "paste"
-version = "1.0.12"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9f746c4065a8fa3fe23974dd82f15431cc8d40779821001404d10d2e79ca7d79"
-
 [[package]]
 name = "percent-encoding"
 version = "2.2.0"
@@ -1385,30 +1114,6 @@ version = "0.2.17"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "5b40af805b3121feab8a3c29f04d8ad262fa8e0561883e7653e024ae4479e6de"
 
-[[package]]
-name = "proc-macro-error"
-version = "1.0.4"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "da25490ff9892aab3fcf7c36f08cfb902dd3e71ca0f9f9517bea02a73a5ce38c"
-dependencies = [
- "proc-macro-error-attr",
- "proc-macro2",
- "quote",
- "syn 1.0.109",
- "version_check",
-]
-
-[[package]]
-name = "proc-macro-error-attr"
-version = "1.0.4"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a1be40180e52ecc98ad80b184934baf3d0d29f979574e439af5a55274b35f869"
-dependencies = [
- "proc-macro2",
- "quote",
- "version_check",
-]
-
 [[package]]
 name = "proc-macro2"
 version = "1.0.64"
@@ -1457,16 +1162,6 @@ dependencies = [
  "getrandom",
 ]
 
-[[package]]
-name = "rand_distr"
-version = "0.4.3"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "32cb0b9bc82b0a0876c2dd994a7e7a2683d3e7390ca40e6886785ef0c7e3ee31"
-dependencies = [
- "num-traits",
- "rand",
-]
-
 [[package]]
 name = "raqote"
 version = "0.8.2"
@@ -1480,12 +1175,6 @@ dependencies = [
  "typed-arena",
 ]
 
-[[package]]
-name = "rawpointer"
-version = "0.2.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "60a357793950651c4ed0f3f52338f53b2f809f32d83a07f72909fa13e4c6c1e3"
-
 [[package]]
 name = "rayon"
 version = "1.7.0"
@@ -1512,7 +1201,6 @@ dependencies = [
 name = "rebar"
 version = "0.2.0"
 dependencies = [
- "bio",
  "chrono",
  "clap",
  "color-eyre",
@@ -1521,8 +1209,9 @@ dependencies = [
  "image",
  "indicatif",
  "indoc",
- "itertools 0.12.0",
+ "itertools",
  "log",
+ "noodles",
  "openssl",
  "petgraph",
  "rand",
@@ -1531,10 +1220,10 @@ dependencies = [
  "reqwest",
  "rustix",
  "rusttype",
- "semver 1.0.19",
+ "semver",
  "serde",
  "serde_json",
- "strum 0.25.0",
+ "strum",
  "tempfile",
  "tokio",
  "zstd",
@@ -1549,35 +1238,6 @@ dependencies = [
  "bitflags 1.3.2",
 ]
 
-[[package]]
-name = "regex"
-version = "1.9.5"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "697061221ea1b4a94a624f67d0ae2bfe4e22b8a17b6a192afb11046542cc8c47"
-dependencies = [
- "aho-corasick",
- "memchr",
- "regex-automata",
- "regex-syntax",
-]
-
-[[package]]
-name = "regex-automata"
-version = "0.3.8"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c2f401f4955220693b56f8ec66ee9c78abffd8d1c4f23dc41a23839eb88f0795"
-dependencies = [
- "aho-corasick",
- "memchr",
- "regex-syntax",
-]
-
-[[package]]
-name = "regex-syntax"
-version = "0.7.5"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "dbb5fb1acd8a1a18b3dd5be62d25485eb770e05afb408a9627d14d451bae12da"
-
 [[package]]
 name = "reqwest"
 version = "0.11.18"
@@ -1621,15 +1281,6 @@ version = "0.1.23"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "d626bb9dae77e28219937af045c257c28bfd3f69333c512553507f5f9798cb76"
 
-[[package]]
-name = "rustc_version"
-version = "0.1.7"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c5f5376ea5e30ce23c03eb77cbe4962b988deead10910c372b226388b594c084"
-dependencies = [
- "semver 0.1.20",
-]
-
 [[package]]
 name = "rustix"
 version = "0.38.25"
@@ -1665,15 +1316,6 @@ version = "1.0.13"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "f91339c0467de62360649f8d3e185ca8de4224ff281f66000de5eb2a77a79041"
 
-[[package]]
-name = "safe_arch"
-version = "0.6.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "794821e4ccb0d9f979512f9c1973480123f9bd62a90d74ab0f9426fcf8f4a529"
-dependencies = [
- "bytemuck",
-]
-
 [[package]]
 name = "schannel"
 version = "0.1.22"
@@ -1712,12 +1354,6 @@ dependencies = [
  "libc",
 ]
 
-[[package]]
-name = "semver"
-version = "0.1.20"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d4f410fedcf71af0345d7607d246e7ad15faaadd49d240ee3b24e5dc21a820ac"
-
 [[package]]
 name = "semver"
 version = "1.0.19"
@@ -1741,7 +1377,7 @@ checksum = "43576ca501357b9b071ac53cdc7da8ef0cbd9493d8df094cd821777ea6e894d3"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.32",
+ "syn",
 ]
 
 [[package]]
@@ -1767,19 +1403,6 @@ dependencies = [
  "serde",
 ]
 
-[[package]]
-name = "simba"
-version = "0.6.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f0b7840f121a46d63066ee7a99fc81dcabbc6105e437cae43528cea199b5a05f"
-dependencies = [
- "approx",
- "num-complex",
- "num-traits",
- "paste",
- "wide",
-]
-
 [[package]]
 name = "simd-adler32"
 version = "0.3.5"
@@ -1805,51 +1428,19 @@ dependencies = [
  "winapi",
 ]
 
-[[package]]
-name = "statrs"
-version = "0.16.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "2d08e5e1748192713cc281da8b16924fb46be7b0c2431854eadc785823e5696e"
-dependencies = [
- "approx",
- "lazy_static",
- "nalgebra",
- "num-traits",
- "rand",
-]
-
 [[package]]
 name = "strsim"
 version = "0.10.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "73473c0e59e6d5812c5dfe2a064a6444949f089e20eec9a2e5506596494e4623"
 
-[[package]]
-name = "strum"
-version = "0.24.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "063e6045c0e62079840579a7e47a355ae92f60eb74daaf156fb1e84ba164e63f"
-
 [[package]]
 name = "strum"
 version = "0.25.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "290d54ea6f91c969195bdbcd7442c8c2a2ba87da8bf60a7ee86a235d4bc1e125"
 dependencies = [
- "strum_macros 0.25.2",
-]
-
-[[package]]
-name = "strum_macros"
-version = "0.24.3"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1e385be0d24f186b4ce2f9982191e7101bb737312ad61c1f2f984f34bcf85d59"
-dependencies = [
- "heck",
- "proc-macro2",
- "quote",
- "rustversion",
- "syn 1.0.109",
+ "strum_macros",
 ]
 
 [[package]]
@@ -1862,7 +1453,7 @@ dependencies = [
  "proc-macro2",
  "quote",
  "rustversion",
- "syn 2.0.32",
+ "syn",
 ]
 
 [[package]]
@@ -1871,17 +1462,6 @@ version = "0.7.16"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "9ac8fb7895b4afa060ad731a32860db8755da3449a47e796d5ecf758db2671d4"
 
-[[package]]
-name = "syn"
-version = "1.0.109"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "72b64191b275b66ffe2469e8af2c1cfe3bafa67b529ead792a6d0160888b4237"
-dependencies = [
- "proc-macro2",
- "quote",
- "unicode-ident",
-]
-
 [[package]]
 name = "syn"
 version = "2.0.32"
@@ -1906,26 +1486,6 @@ dependencies = [
  "windows-sys 0.48.0",
 ]
 
-[[package]]
-name = "thiserror"
-version = "1.0.40"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "978c9a314bd8dc99be594bc3c175faaa9794be04a5a5e153caba6915336cebac"
-dependencies = [
- "thiserror-impl",
-]
-
-[[package]]
-name = "thiserror-impl"
-version = "1.0.40"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f9456a42c5b0d803c8cd86e73dd7cc9edd429499f37a3550d286d5e86720569f"
-dependencies = [
- "proc-macro2",
- "quote",
- "syn 2.0.32",
-]
-
 [[package]]
 name = "tinyvec"
 version = "1.6.0"
@@ -1966,7 +1526,7 @@ checksum = "630bdcf245f78637c13ec01ffae6187cca34625e8c63150d424b59e55af2675e"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.32",
+ "syn",
 ]
 
 [[package]]
@@ -2019,12 +1579,6 @@ dependencies = [
  "once_cell",
 ]
 
-[[package]]
-name = "triple_accel"
-version = "0.4.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "22048bc95dfb2ffd05b1ff9a756290a009224b60b2f0e7525faeee7603851e63"
-
 [[package]]
 name = "try-lock"
 version = "0.2.4"
@@ -2043,12 +1597,6 @@ version = "2.0.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "6af6ae20167a9ece4bcb41af5b80f8a1f1df981f6391189ce00fd257af04126a"
 
-[[package]]
-name = "typenum"
-version = "1.16.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "497961ef93d974e23eb6f433eb5fe1b7930b659f06d12dec6fc44a8f554c0bba"
-
 [[package]]
 name = "unicode-bidi"
 version = "0.3.13"
@@ -2093,21 +1641,6 @@ version = "0.2.15"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "accd4ea62f7bb7a82fe23066fb0957d48ef677f6eeb8215f372f52e48bb32426"
 
-[[package]]
-name = "vec_map"
-version = "0.8.2"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f1bddf1187be692e79c5ffeab891132dfb0f236ed36a43c7ed39f1165ee20191"
-dependencies = [
- "serde",
-]
-
-[[package]]
-name = "version_check"
-version = "0.9.4"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "49874b5167b65d7193b8aba1567f5c7d93d001cafc34600cee003eda787e483f"
-
 [[package]]
 name = "want"
 version = "0.3.0"
@@ -2145,7 +1678,7 @@ dependencies = [
  "once_cell",
  "proc-macro2",
  "quote",
- "syn 2.0.32",
+ "syn",
  "wasm-bindgen-shared",
 ]
 
@@ -2179,7 +1712,7 @@ checksum = "e128beba882dd1eb6200e1dc92ae6c5dbaa4311aa7bb211ca035779e5efc39f8"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.32",
+ "syn",
  "wasm-bindgen-backend",
  "wasm-bindgen-shared",
 ]
@@ -2200,16 +1733,6 @@ dependencies = [
  "wasm-bindgen",
 ]
 
-[[package]]
-name = "wide"
-version = "0.7.9"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5cd0496a71f3cc6bc4bf0ed91346426a5099e93d89807e663162dc5a1069ff65"
-dependencies = [
- "bytemuck",
- "safe_arch",
-]
-
 [[package]]
 name = "winapi"
 version = "0.3.9"
diff --git a/Cargo.toml b/Cargo.toml
index de42cdb..075d46f 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -4,7 +4,6 @@ version = "0.2.0"
 edition = "2021"
 
 [dependencies]
-bio             = { version = "1.1.0",   default-features = false }
 chrono          = { version = "0.4.31",  default-features = false, features = ["clock", "serde"] }
 clap            = { version = "4.2.7",   default-features = true,  features = ["derive", "string"] }
 color-eyre      = { version = "0.6.2",   default-features = false }
@@ -15,10 +14,11 @@ indicatif       = { version = "0.17.5",  default-features = false, features = ["
 indoc           = { version = "2.0.4",   default-features = false }
 itertools       = { version = "0.12.0",  default-features = false, features = ["use_std"] }
 log             = { version = "0.4.17",  default-features = false }
+noodles         = { version = "0.59.0", default-features = false, features = ["core", "fasta"]}
 openssl         = { version = "0.10.60", default-features = false, features = ["vendored"]}
 petgraph        = { version = "0.6.3",   default-features = false, features = ["serde-1"] }
 raqote          = { version = "0.8.2",   default-features = false, features = ["png"]}
-rand            = { version = "0.8.5",   default-features = false }
+rand            = { version = "0.8.5", default-features = false, features = ["std", "std_rng"] }
 rayon           = { version = "1.7.0",   default-features = false }
 reqwest         = { version = "0.11.18", default-features = true,  features = ["json"] }
 rustix          = { version = "0.38.25", default-features = false }
diff --git a/src/dataset/load.rs b/src/dataset/load.rs
index c5f9f3e..ec440a9 100644
--- a/src/dataset/load.rs
+++ b/src/dataset/load.rs
@@ -3,10 +3,12 @@ use crate::dataset::attributes::{Name, Summary, Tag};
 use crate::dataset::Dataset;
 use crate::phylogeny::Phylogeny;
 use crate::sequence::{read_reference, Sequence, Substitution};
-use bio::io::fasta;
-use color_eyre::eyre::{eyre, Report, Result, WrapErr};
+use color_eyre::eyre::{Report, Result};
 use log::{info, warn};
+use noodles::fasta;
 use std::collections::BTreeMap;
+use std::fs::File;
+use std::io::BufReader;
 use std::path::Path;
 
 // ----------------------------------------------------------------------------
@@ -88,9 +90,8 @@ pub fn parse_populations(
     Report,
 > {
     // read in populations from fasta
-    let populations_reader = fasta::Reader::from_file(populations_path)
-        .map_err(|e| eyre!(e))
-        .wrap_err(format!("Failed to read file: {populations_path:?}"))?;
+    let mut reader =
+        File::open(populations_path).map(BufReader::new).map(fasta::Reader::new)?;
 
     // read in reference from fasta
     let reference = read_reference(reference_path, mask)?;
@@ -98,15 +99,16 @@ pub fn parse_populations(
     let mut populations = BTreeMap::new();
     let mut mutations = BTreeMap::new();
 
-    for result in populations_reader.records() {
+    reader.records().try_for_each(|result| {
         let record = result?;
         let sequence = Sequence::from_record(record, Some(&reference), mask)?;
         populations.insert(sequence.id.clone(), sequence.clone());
 
-        for sub in sequence.substitutions {
+        sequence.substitutions.into_iter().for_each(|sub| {
             mutations.entry(sub).or_insert(Vec::new()).push(sequence.id.clone());
-        }
-    }
+        });
+        Ok::<(), Report>(())
+    })?;
 
     Ok((populations, mutations))
 }
diff --git a/src/dataset/mod.rs b/src/dataset/mod.rs
index 0e4efc0..7b86cbd 100644
--- a/src/dataset/mod.rs
+++ b/src/dataset/mod.rs
@@ -12,6 +12,7 @@ use color_eyre::eyre::{eyre, Report, Result, WrapErr};
 use indoc::formatdoc;
 use itertools::Itertools;
 use log::debug;
+use noodles::fasta;
 use serde::{Deserialize, Serialize};
 use std::collections::BTreeMap;
 use std::default::Default;
@@ -84,13 +85,15 @@ impl Dataset {
             })
             .join("");
 
-        // create bio record
-        let description = None;
-        let record =
-            bio::io::fasta::Record::with_attrs(name, description, consensus.as_bytes());
+        // create new fasta record
+        let definition = fasta::record::Definition::new(name, None);
+        let sequence = fasta::record::Sequence::from(consensus.as_bytes().to_vec());
+        let record = fasta::Record::new(definition, sequence);
+
         // parse and create Sequence record
         // dataset is already masked, no need
         let mask = Vec::new();
+
         let sequence = Sequence::from_record(record, Some(&self.reference), &mask)?;
 
         Ok(sequence)
diff --git a/src/dataset/sarscov2/phylogeny.rs b/src/dataset/sarscov2/phylogeny.rs
index c83857e..e5efe5b 100644
--- a/src/dataset/sarscov2/phylogeny.rs
+++ b/src/dataset/sarscov2/phylogeny.rs
@@ -1,10 +1,12 @@
 use crate::{dataset, phylogeny::Phylogeny, utils::table::Table};
-use bio::io::fasta;
 use color_eyre::eyre::{eyre, Report, Result, WrapErr};
 use color_eyre::Help;
 use itertools::Itertools;
 use log::{debug, info, warn};
+use noodles::fasta;
 use std::collections::BTreeMap;
+use std::fs::File;
+use std::io::BufReader;
 use std::path::Path;
 
 pub async fn build(
@@ -92,19 +94,18 @@ pub async fn build(
     // read populations fasta, to check if any lineages are missing in notes
     let populations_path = &summary.populations.local_path;
     let populations_file_name = populations_path.file_name().unwrap().to_str().unwrap();
-    let alignment_reader = fasta::Reader::from_file(populations_path)
-        .map_err(|e| eyre!(e))
-        .wrap_err("Failed to read file: {populations_path:?}")?;
+    let file = File::open(populations_path);
+    let mut reader = file.map(BufReader::new).map(fasta::Reader::new)?;
 
     // keep track of population names in alignment, cross-reference against
     // lineage notes + alias_key later
     let mut alignment_populations = Vec::new();
-    for result in alignment_reader.records() {
-        let record =
-            result.wrap_err(eyre!("Failed to parse file: {populations_path:?}"))?;
-        let lineage = record.id().to_string();
+    reader.records().try_for_each(|result| {
+        let record = result.wrap_err(eyre!("Failed to parse fasta record."))?;
+        let lineage = record.name().to_string();
         alignment_populations.push(lineage);
-    }
+        Ok::<(), Report>(())
+    })?;
 
     // ------------------------------------------------------------------------
     // Parent Child Relationships
diff --git a/src/run/mod.rs b/src/run/mod.rs
index 7815b72..5b9195f 100644
--- a/src/run/mod.rs
+++ b/src/run/mod.rs
@@ -6,14 +6,14 @@ use crate::recombination;
 use crate::dataset::{attributes::Name, SearchResult};
 use crate::recombination::Recombination;
 use crate::sequence::Sequence;
-use bio::io::fasta;
-use color_eyre::eyre::{eyre, Report, Result, WrapErr};
+use color_eyre::eyre::{Report, Result, WrapErr};
 use indicatif::{style::ProgressStyle, ProgressBar};
 use itertools::Itertools;
 use log::{debug, info, warn};
+use noodles::fasta;
 use rayon::iter::{IntoParallelRefIterator, ParallelIterator};
 use std::fs::{create_dir_all, File};
-use std::io::Write;
+use std::io::{BufReader, Write};
 
 /// Run rebar on input alignment and/or dataset population(s)
 pub fn run(args: &mut cli::run::Args) -> Result<(), Report> {
@@ -111,11 +111,10 @@ pub fn run(args: &mut cli::run::Args) -> Result<(), Report> {
 
     if let Some(alignment) = &args.input.alignment {
         info!("Loading query alignment: {:?}", alignment);
-        let alignment_reader = fasta::Reader::from_file(alignment)
-            .map_err(|e| eyre!(e))
-            .wrap_err("Failed to read file: {alignment:?}")?;
+        let file = File::open(alignment);
+        let mut reader = file.map(BufReader::new).map(fasta::Reader::new)?;
 
-        for result in alignment_reader.records() {
+        for result in reader.records() {
             let record = result.wrap_err("Unable to parse alignment: {alignment:?}")?;
             let sequence =
                 Sequence::from_record(record, Some(&dataset.reference), &args.mask)?;
diff --git a/src/sequence/mod.rs b/src/sequence/mod.rs
index 3d37fed..f222b30 100644
--- a/src/sequence/mod.rs
+++ b/src/sequence/mod.rs
@@ -1,11 +1,13 @@
 pub mod parsimony;
 
-use bio::io::fasta;
-use color_eyre::eyre::{eyre, Report, Result, WrapErr};
+use color_eyre::eyre::{eyre, ContextCompat, Report, Result, WrapErr};
 use color_eyre::Help;
+use noodles::{core::Position, fasta};
 use serde::{Deserialize, Serialize};
 use std::cmp::Ordering;
 use std::default::Default;
+use std::fs::File;
+use std::io::BufReader;
 use std::path::Path;
 use std::str::FromStr;
 
@@ -140,20 +142,35 @@ impl Sequence {
         }
     }
 
+    /// Parse fasta record into a rebar sequence.
     pub fn from_record(
-        record: bio::io::fasta::Record,
+        record: fasta::Record,
         reference: Option<&Sequence>,
         mask: &Vec<usize>,
     ) -> Result<Self, Report> {
         let mut sample = Sequence::new();
-        sample.id = record.id().to_string();
-        sample.seq = record.seq().iter().map(|b| *b as char).collect();
+
+        // parse fasta::Record into rebar Sequence
+        let id = record.name().to_string();
+
+        // convert sequence to vec of bases, noodle positions are 1-based!
+        let start = Position::try_from(1).unwrap();
+        let seq: Vec<char> = record
+            .sequence()
+            .get(start..)
+            .context(format!("Failed to parse sequence record {}", &sample.id))?
+            .iter()
+            .map(|b| *b as char)
+            .collect();
+        let sample_len = seq.len();
+        sample.id = id.clone();
+        sample.seq = seq;
 
         // check mask coord
         for bases in mask {
             if *bases > sample.seq.len() {
                 return Err(
-                    eyre!("5' and 3' masking ({mask:?}) is incompatible with sequence length {}", sample.seq.len())
+                    eyre!("5' and 3' masking ({mask:?}) is incompatible with {id} sequence length {sample_len}")
                     .suggestion("Please change your --mask parameter.")
                     .suggestion("Maybe you want to disable masking all together with --mask 0,0 ?")
                 );
@@ -161,15 +178,11 @@ impl Sequence {
         }
 
         if let Some(reference) = reference {
-            if sample.seq.len() != reference.seq.len() {
+            let ref_len = reference.seq.len();
+            if sample_len != ref_len {
                 return Err(
-                    eyre!(
-                        "Reference sequence ({ref_len}) and {record_id} ({record_len}) are different lengths!",
-                        ref_len=reference.seq.len(),
-                        record_id=sample.id,
-                        record_len=sample.seq.len(),
-                    )
-                    .suggestion("Are you sure your --alignment is aligned correctly?")
+                    eyre!("Reference and {id} are different lengths ({ref_len} vs {sample_len})!")
+                    .suggestion(format!("Are you sure {id} is aligned correctly?"))
                 );
             }
             sample.genome_length = reference.seq.len();
@@ -234,7 +247,7 @@ impl Sequence {
 /// Read first record of fasta path into sequence record.
 pub fn read_reference(path: &Path, mask: &Vec<usize>) -> Result<Sequence, Report> {
     // start reading in the reference as fasta, raise error if file doesn't exist
-    let reader = fasta::Reader::from_file(path).expect("Unable to read reference");
+    let mut reader = File::open(path).map(BufReader::new).map(fasta::Reader::new)?;
 
     // parse just the first record from the reference
     // 1. raise error if record iterator doesn't work