@@ -10,32 +10,30 @@ Wei Shen\*, Botond Sipos, and Liuyang Zhao. 2024. SeqKit2: A Swiss Army Knife fo
1010
1111## Current Version
1212
13- - [ SeqKit v2.10.1] ( https://github.com/shenwei356/seqkit/releases/tag/v2.10.1 ) - 2025-08-19
14- [ ![ 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 )
15- - ` seqkit seq ` :
16- - fix validating sequences: it failed to report an error when the invalid sequence is not the last one in the input. [ #536 ] ( https://github.com/shenwei356/seqkit/issues/536 )
17- - ` seqkit stats ` :
18- - fix decimal places of some fields when using ` -T ` .
19- - ` seqkit fx2tab ` :
20- - fix the calculation of GC content (` --gc ` ). Previously, the denominator was the total sequence length, which could lead to inaccuracies due to the potential presence of gaps in the sequence. [ #515 ] ( https://github.com/shenwei356/seqkit/issues/515 )
21- - ` seqkit sample ` :
22- - fix ` -n ` for in-memory mode. [ #518 ] ( https://github.com/shenwei356/seqkit/issues/518 )
23- - ` seqkit subseq ` :
24- - fix the bug that subseq --feature is not case insensitive. [ #523 ] ( https://github.com/shenwei356/seqkit/issues/523 )
25- - ` seqkit grep/locate/mutate ` :
26- - update help message for ` -p/--pattern ` , to show how to set multiple values. [ #527 ] ( https://github.com/shenwei356/seqkit/pull/527 ) by @corneliusroemer
13+ - [ SeqKit v2.11.0] ( https://github.com/shenwei356/seqkit/releases/tag/v2.11.0 ) - 2025-11-20
14+ [ ![ 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 )
15+ - ` seqkit ` :
16+ - ** fix reading records with both empty id and sequence** . [ #550 ] ( https://github.com/shenwei356/seqkit/issues/550 )
17+ - check if the output file name equals to one of the input files. [ #541 ] ( https://github.com/shenwei356/seqkit/issues/541 )
18+ - ` seqkit split2 ` :
19+ - add a new flag ` -N, --seqid-as-filename ` to use the first sequence ID as the file name.
20+ E.g., using ` -N -s 1 ` is equal to ` seqkit split --by-id ` , but it's much faster and uses less memory.
21+ - ` seqkit head ` :
22+ - add a new flag ` -l, --length ` to print heading FASTA/Q records with total sequence length >= N, e.g., ` -l 2G ` .
23+ - ` seqkit replace ` :
24+ - add a new replacement symbol ` {uuid} ` for random UUID. [ #552 ] ( https://github.com/shenwei356/seqkit/issues/552 )
25+
2726
2827### Links
2928
30- | OS | Arch | File, 中国镜像 | Download Count |
31- | :------ | :--------- | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | :----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
32- | Linux | 32-bit | [ seqkit_linux_386.tar.gz] ( https://github.com/shenwei356/seqkit/releases/download/v2.10.1/seqkit_linux_386.tar.gz ) , <br /> [ 中国镜像] ( http://app.shenwei.me/data/seqkit/seqkit_linux_386.tar.gz ) | [ ![ Github Releases (by Asset)] ( https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_linux_386.tar.gz.svg?maxAge=3600 )] ( https://github.com/shenwei356/seqkit/releases/download/v2.10.1/seqkit_linux_386.tar.gz ) |
33- | Linux | ** 64-bit** | [ ** seqkit_linux_amd64.tar.gz** ] ( https://github.com/shenwei356/seqkit/releases/download/v2.10.1/seqkit_linux_amd64.tar.gz ) , <br /> [ 中国镜像] ( http://app.shenwei.me/data/seqkit/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/v2.10.1/seqkit_linux_amd64.tar.gz ) |
34- | Linux | ** arm64** | [ ** seqkit_linux_arm64.tar.gz** ] ( https://github.com/shenwei356/seqkit/releases/download/v2.10.1/seqkit_linux_arm64.tar.gz ) , <br /> [ 中国镜像] ( http://app.shenwei.me/data/seqkit/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/v2.10.1/seqkit_linux_arm64.tar.gz ) |
35- | macOS | ** 64-bit** | [ ** seqkit_darwin_amd64.tar.gz** ] ( https://github.com/shenwei356/seqkit/releases/download/v2.10.1/seqkit_darwin_amd64.tar.gz ) , <br /> [ 中国镜像] ( http://app.shenwei.me/data/seqkit/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/v2.10.1/seqkit_darwin_amd64.tar.gz ) |
36- | macOS | ** arm64** | [ ** seqkit_darwin_arm64.tar.gz** ] ( https://github.com/shenwei356/seqkit/releases/download/v2.10.1/seqkit_darwin_arm64.tar.gz ) , <br /> [ 中国镜像] ( http://app.shenwei.me/data/seqkit/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/v2.10.1/seqkit_darwin_arm64.tar.gz ) |
37- | Windows | 32-bit | [ seqkit_windows_386.exe.tar.gz] ( https://github.com/shenwei356/seqkit/releases/download/v2.10.1/seqkit_windows_386.exe.tar.gz ) , <br /> [ 中国镜像] ( http://app.shenwei.me/data/seqkit/seqkit_windows_386.exe.tar.gz ) | [ ![ Github Releases (by Asset)] ( https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_windows_386.exe.tar.gz.svg?maxAge=3600 )] ( https://github.com/shenwei356/seqkit/releases/download/v2.10.1/seqkit_windows_386.exe.tar.gz ) |
38- | Windows | ** 64-bit** | [ ** seqkit_windows_amd64.exe.tar.gz** ] ( https://github.com/shenwei356/seqkit/releases/download/v2.10.1/seqkit_windows_amd64.exe.tar.gz ) , <br /> [ 中国镜像] ( http://app.shenwei.me/data/seqkit/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/v2.10.1/seqkit_windows_amd64.exe.tar.gz ) |
29+ | OS | Arch | File | Download Count |
30+ | :------ | :------| :------------------------------------------------------------------------------------------------------------------------------------- | :-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
31+ | 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 ) |
32+ | 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 ) |
33+ | 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 ) |
34+ | 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 ) |
35+ | 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 ) |
36+ | 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 ) |
3937
4038
4139* Notes*
@@ -95,9 +93,9 @@ Run the following commands:
9593 # ------------------- install golang -----------------
9694
9795 # download Go from https://go.dev/dl
98- wget https://go.dev/dl/go1.25.0 .linux-amd64.tar.gz
96+ wget https://go.dev/dl/go1.25.4 .linux-amd64.tar.gz
9997
100- tar -zxf go1.25.0 .linux-amd64.tar.gz -C $HOME/
98+ tar -zxf go1.25.4 .linux-amd64.tar.gz -C $HOME/
10199
102100 # or
103101 # echo "export PATH=$PATH:$HOME/go/bin" >> ~/.bashrc
@@ -110,7 +108,7 @@ Run the following commands:
110108 cd seqkit/seqkit/
111109
112110 # optionally choose a release
113- # git check v2.10.1
111+ # git check v2.11.0
114112
115113 export GOEXPERIMENT=greenteagc # for go1.25
116114 go build -trimpath -ldflags="-s -w" -tags netgo
@@ -151,6 +149,20 @@ fish:
151149
152150## Release history
153151
152+ - [ SeqKit v2.10.1] ( https://github.com/shenwei356/seqkit/releases/tag/v2.10.1 ) - 2025-08-19
153+ [ ![ 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 )
154+ - ` seqkit seq ` :
155+ - fix validating sequences: it failed to report an error when the invalid sequence is not the last one in the input. [ #536 ] ( https://github.com/shenwei356/seqkit/issues/536 )
156+ - ` seqkit stats ` :
157+ - fix decimal places of some fields when using ` -T ` .
158+ - ` seqkit fx2tab ` :
159+ - fix the calculation of GC content (` --gc ` ). Previously, the denominator was the total sequence length, which could lead to inaccuracies due to the potential presence of gaps in the sequence. [ #515 ] ( https://github.com/shenwei356/seqkit/issues/515 )
160+ - ` seqkit sample ` :
161+ - fix ` -n ` for in-memory mode. [ #518 ] ( https://github.com/shenwei356/seqkit/issues/518 )
162+ - ` seqkit subseq ` :
163+ - fix the bug that subseq --feature is not case insensitive. [ #523 ] ( https://github.com/shenwei356/seqkit/issues/523 )
164+ - ` seqkit grep/locate/mutate ` :
165+ - update help message for ` -p/--pattern ` , to show how to set multiple values. [ #527 ] ( https://github.com/shenwei356/seqkit/pull/527 ) by @corneliusroemer
154166- [ SeqKit v2.10.0] ( https://github.com/shenwei356/seqkit/releases/tag/v2.10.0 ) - 2025-03-12
155167[ ![ Github Releases (by Release)] ( https://img.shields.io/github/downloads/shenwei356/seqkit/v2.10.0/total.svg )] ( https://github.com/shenwei356/seqkit/releases/tag/v2.10.0 )
156168 - ` seqkit ` :
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