v2.12.0

Author: shenwei356

CHANGELOG.md

@@ -1,11 +1,13 @@
-- [SeqKit v2.12.0](https://github.com/shenwei356/seqkit/releases/tag/v2.12.0) - 2025-xx-xx
+- [SeqKit v2.12.0](https://github.com/shenwei356/seqkit/releases/tag/v2.12.0) - 2025-12-04
 [![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/seqkit/v2.12.0/total.svg)](https://github.com/shenwei356/seqkit/releases/tag/v2.12.0)
     - `seqkit grep`:
         - `-p/--pattern` accepts empty charactor (`""`) now. So it's able to **search records with empty IDs or sequences**. [#558](https://github.com/shenwei356/seqkit/issues/558)
     - `seqkit split2`:
         - fix a bug introduced in v2.11.0: `--by-part-prefix` options has no effect. [#554](https://github.com/shenwei356/seqkit/issues/554)
     - `seqkit replace`:
         - `{uuid}`: use the time-sortable UUIDv7 to replace v4.
+    - `seqkit stats/fx2tab`:
+        - add information about how the average quality is computed. [#448](https://github.com/shenwei356/seqkit/issues/448)
 - [SeqKit v2.11.0](https://github.com/shenwei356/seqkit/releases/tag/v2.11.0) - 2025-11-20
 [![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/seqkit/v2.11.0/total.svg)](https://github.com/shenwei356/seqkit/releases/tag/v2.11.0)
     - `seqkit`:

doc/docs/download.md

@@ -10,30 +10,27 @@ Wei Shen\*, Botond Sipos, and Liuyang Zhao. 2024. SeqKit2: A Swiss Army Knife fo
 
 ## Current Version
 
-- [SeqKit v2.11.0](https://github.com/shenwei356/seqkit/releases/tag/v2.11.0) - 2025-11-20
-[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/seqkit/v2.11.0/total.svg)](https://github.com/shenwei356/seqkit/releases/tag/v2.11.0)
-    - `seqkit`:
-        - **fix reading records with both empty id and sequence**. [#550](https://github.com/shenwei356/seqkit/issues/550)
-        - check if the output file name equals to one of the input files. [#541](https://github.com/shenwei356/seqkit/issues/541)
+- [SeqKit v2.12.0](https://github.com/shenwei356/seqkit/releases/tag/v2.12.0) - 2025-12-04
+[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/seqkit/v2.12.0/total.svg)](https://github.com/shenwei356/seqkit/releases/tag/v2.12.0)
+    - `seqkit grep`:
+        - `-p/--pattern` accepts empty charactor (`""`) now. So it's able to **search records with empty IDs or sequences**. [#558](https://github.com/shenwei356/seqkit/issues/558)
     - `seqkit split2`:
-        - add a new flag `-N, --seqid-as-filename` to use the first sequence ID as the file name. 
-        E.g., using `-N -s 1` is equal to `seqkit split --by-id`, but it's much faster and uses less memory.
-    - `seqkit head`:
-        - add a new flag `-l, --length` to print heading FASTA/Q records with total sequence length >= N, e.g., `-l 2G`.
+        - fix a bug introduced in v2.11.0: `--by-part-prefix` options has no effect. [#554](https://github.com/shenwei356/seqkit/issues/554)
     - `seqkit replace`:
-        - add a new replacement symbol `{uuid}` for random UUID. [#552](https://github.com/shenwei356/seqkit/issues/552)
-
+        - `{uuid}`: use the time-sortable UUIDv7 to replace v4.
+    - `seqkit stats/fx2tab`:
+        - add information about how the average quality is computed. [#448](https://github.com/shenwei356/seqkit/issues/448)
 
 ### Links
 
 | OS      | Arch   | File                                                                                                                                   | Download Count                                                                                                                                                                                                                                |
 | :------ | :------| :------------------------------------------------------------------------------------------------------------------------------------- | :-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| Linux   | 64-bit | [seqkit_linux_amd64.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v2.11.0/seqkit_linux_amd64.tar.gz)              | [![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_linux_amd64.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/seqkit/releases/download/v2.11.0/seqkit_linux_amd64.tar.gz)             |
-| Linux   | arm64  | [seqkit_linux_arm64.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v2.11.0/seqkit_linux_arm64.tar.gz)              | [![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_linux_arm64.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/seqkit/releases/download/v2.11.0/seqkit_linux_arm64.tar.gz)             |
-| macOS   | 64-bit | [seqkit_darwin_amd64.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v2.11.0/seqkit_darwin_amd64.tar.gz)            | [![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_darwin_amd64.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/seqkit/releases/download/v2.11.0/seqkit_darwin_amd64.tar.gz)           |
-| macOS   | arm64  | [seqkit_darwin_arm64.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v2.11.0/seqkit_darwin_arm64.tar.gz)            | [![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_darwin_arm64.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/seqkit/releases/download/v2.11.0/seqkit_darwin_arm64.tar.gz)           |
-| Windows | 64-bit | [seqkit_windows_amd64.exe.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v2.11.0/seqkit_windows_amd64.exe.tar.gz)  | [![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_windows_amd64.exe.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/seqkit/releases/download/v2.11.0/seqkit_windows_amd64.exe.tar.gz) |
-| FreeBSD | 64-bit | [seqkit_freebsd_amd64.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v2.11.0/seqkit_freebsd_amd64.tar.gz)          | [![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_freebsd_amd64.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/seqkit/releases/download/v2.11.0/seqkit_freebsd_amd64.tar.gz)         |
+| Linux   | 64-bit | [seqkit_linux_amd64.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v2.12.0/seqkit_linux_amd64.tar.gz)              | [![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_linux_amd64.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/seqkit/releases/download/v2.12.0/seqkit_linux_amd64.tar.gz)             |
+| Linux   | arm64  | [seqkit_linux_arm64.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v2.12.0/seqkit_linux_arm64.tar.gz)              | [![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_linux_arm64.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/seqkit/releases/download/v2.12.0/seqkit_linux_arm64.tar.gz)             |
+| macOS   | 64-bit | [seqkit_darwin_amd64.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v2.12.0/seqkit_darwin_amd64.tar.gz)            | [![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_darwin_amd64.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/seqkit/releases/download/v2.12.0/seqkit_darwin_amd64.tar.gz)           |
+| macOS   | arm64  | [seqkit_darwin_arm64.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v2.12.0/seqkit_darwin_arm64.tar.gz)            | [![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_darwin_arm64.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/seqkit/releases/download/v2.12.0/seqkit_darwin_arm64.tar.gz)           |
+| Windows | 64-bit | [seqkit_windows_amd64.exe.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v2.12.0/seqkit_windows_amd64.exe.tar.gz)  | [![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_windows_amd64.exe.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/seqkit/releases/download/v2.12.0/seqkit_windows_amd64.exe.tar.gz) |
+| FreeBSD | 64-bit | [seqkit_freebsd_amd64.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v2.12.0/seqkit_freebsd_amd64.tar.gz)          | [![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_freebsd_amd64.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/seqkit/releases/download/v2.12.0/seqkit_freebsd_amd64.tar.gz)         |
 
 
 *Notes*
@@ -93,9 +90,9 @@ Run the following commands:
     # ------------------- install golang -----------------
 
     # download Go from https://go.dev/dl
-    wget https://go.dev/dl/go1.25.4.linux-amd64.tar.gz
+    wget https://go.dev/dl/go1.25.5.linux-amd64.tar.gz
 
-    tar -zxf go1.25.4.linux-amd64.tar.gz -C $HOME/
+    tar -zxf go1.25.5.linux-amd64.tar.gz -C $HOME/
 
     # or 
     #   echo "export PATH=$PATH:$HOME/go/bin" >> ~/.bashrc
@@ -149,6 +146,19 @@ fish:
 
 ## Release history
 
+        
+- [SeqKit v2.11.0](https://github.com/shenwei356/seqkit/releases/tag/v2.11.0) - 2025-11-20
+[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/seqkit/v2.11.0/total.svg)](https://github.com/shenwei356/seqkit/releases/tag/v2.11.0)
+    - `seqkit`:
+        - **fix reading records with both empty id and sequence**. [#550](https://github.com/shenwei356/seqkit/issues/550)
+        - check if the output file name equals to one of the input files. [#541](https://github.com/shenwei356/seqkit/issues/541)
+    - `seqkit split2`:
+        - add a new flag `-N, --seqid-as-filename` to use the first sequence ID as the file name. 
+        E.g., using `-N -s 1` is equal to `seqkit split --by-id`, but it's much faster and uses less memory.
+    - `seqkit head`:
+        - add a new flag `-l, --length` to print heading FASTA/Q records with total sequence length >= N, e.g., `-l 2G`.
+    - `seqkit replace`:
+        - add a new replacement symbol `{uuid}` for random UUID. [#552](https://github.com/shenwei356/seqkit/issues/552)
 - [SeqKit v2.10.1](https://github.com/shenwei356/seqkit/releases/tag/v2.10.1) - 2025-08-19
 [![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/seqkit/v2.10.1/total.svg)](https://github.com/shenwei356/seqkit/releases/tag/v2.10.1)
     - `seqkit seq`:

doc/docs/usage.md

@@ -698,7 +698,12 @@ Columns:
   14. N50_num   N50_num or L50. https://en.wikipedia.org/wiki/N50,_L50,_and_related_statistics#L50
   15. Q20(%)    percentage of bases with the quality score greater than 20
   16. Q30(%)    percentage of bases with the quality score greater than 30
-  17. AvgQual   average quality
+  17. AvgQual   average quality.
+                Attention: It's not the arithmetic average of quartiles (some tools do that).
+                How to computate: 1) take the qscore for each base, 2) convert it back to
+                an error probability, 3) take the mean of those, 4) and then convert that
+                mean error back into a qscore.
+                Reference: https://github.com/shenwei356/seqkit/issues/448
   18. GC(%)     percentage of GC content
   19. sum_n     number of ambitious letters (N, n, X, x)
   
@@ -1232,6 +1237,11 @@ like sequence length, GC content/GC skew.
 Attention:
   1. Fixed three columns (ID, sequence, quality) are outputted for either FASTA
      or FASTQ, except when flag -n/--name is on. This is for format compatibility.
+  2. The average quality is not the arithmetic average of quartiles (some tools do that).
+     How to computate: 1) take the qscore for each base, 2) convert it back to
+     an error probability, 3) take the mean of those, 4) and then convert that
+     mean error back into a qscore.
+     Reference: https://github.com/shenwei356/seqkit/issues/448
 
 Usage:
   seqkit fx2tab [flags] 

seqkit/cmd/amplicon.go

@@ -1,4 +1,4 @@
-// Copyright © 2016 Wei Shen <shenwei356@gmail.com>
+// Copyright © 2016-2026 Wei Shen <shenwei356@gmail.com>
 //
 // Permission is hereby granted, free of charge, to any person obtaining a copy
 // of this software and associated documentation files (the "Software"), to deal

seqkit/cmd/bed.go

@@ -1,4 +1,4 @@
-// Copyright © 2016-2019 Wei Shen <shenwei356@gmail.com>
+// Copyright © 2016-2026 Wei Shen <shenwei356@gmail.com>
 //
 // Permission is hereby granted, free of charge, to any person obtaining a copy
 // of this software and associated documentation files (the "Software"), to deal

seqkit/cmd/common.go

@@ -1,4 +1,4 @@
-// Copyright © 2016-2023 Wei Shen <shenwei356@gmail.com>
+// Copyright © 2016-2026 Wei Shen <shenwei356@gmail.com>
 //
 // Permission is hereby granted, free of charge, to any person obtaining a copy
 // of this software and associated documentation files (the "Software"), to deal

seqkit/cmd/concat.go

@@ -1,4 +1,4 @@
-// Copyright © 2016-2019 Wei Shen <shenwei356@gmail.com>
+// Copyright © 2016-2026 Wei Shen <shenwei356@gmail.com>
 //
 // Permission is hereby granted, free of charge, to any person obtaining a copy
 // of this software and associated documentation files (the "Software"), to deal

seqkit/cmd/convert.go

@@ -1,4 +1,4 @@
-// Copyright © 2016-2019 Wei Shen <shenwei356@gmail.com>
+// Copyright © 2016-2026 Wei Shen <shenwei356@gmail.com>
 //
 // Permission is hereby granted, free of charge, to any person obtaining a copy
 // of this software and associated documentation files (the "Software"), to deal

seqkit/cmd/dup.go

@@ -1,4 +1,4 @@
-// Copyright © 2016-2019 Wei Shen <shenwei356@gmail.com>
+// Copyright © 2016-2026 Wei Shen <shenwei356@gmail.com>
 //
 // Permission is hereby granted, free of charge, to any person obtaining a copy
 // of this software and associated documentation files (the "Software"), to deal

seqkit/cmd/fa2fq.go

@@ -1,4 +1,4 @@
-// Copyright © 2016-2021 Wei Shen <shenwei356@gmail.com>
+// Copyright © 2016-2026 Wei Shen <shenwei356@gmail.com>
 //
 // Permission is hereby granted, free of charge, to any person obtaining a copy
 // of this software and associated documentation files (the "Software"), to deal